Commands used in the analysis of Fusarium oxysporum isolates ex. pea
To update profiles in future:
cp /home/armita/generic_profiles/2016-07-28/.generic_profile ~/.profile
(change the dates for future updates)
To look at your profile:
less ~/.profile OR cd /home/armita less .profile
Commands used during analysis of the F.oxysporum f.sp pisi genome. Note - all this work was performed in the directory:
mkdir -p /home/groups/harrisonlab/project_files/fusarium_ex_pea
cd /home/groups/harrisonlab/project_files/fusarium_ex_peaThis makes a new directory in project files called fusarium_ex_pea and then changes directory to this new directory
The following is a summary of the work presented in this Readme: Data organisation:
- Preparing data
Draft Genome assembly - Data qc
- Genome assembly
- Repeatmasking
- Gene prediction
- Functional annotation Genome analysis
- Homology between predicted genes & published effectors
#Data organisation
Data was copied from the raw_data repository to a local directory for assembly and annotation.
RawDatDir=/home/groups/harrisonlab/raw_data/raw_seq/fusarium/HAPI_seq_3/
ProjectDir=/home/groups/harrisonlab/project_files/fusarium_ex_pea
mkdir -p $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG3/F
mkdir -p $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG3/R
mkdir -p $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG18/F
mkdir -p $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG18/R
cp $RawDatDir/FoxysporumPG3_S3_L001_R1_001.fastq.gz $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG3/F/.
cp $RawDatDir/FoxysporumPG3_S3_L001_R2_001.fastq.gz $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG3/R/.
cp $RawDatDir/FoxysporumPG18_S4_L001_R1_001.fastq.gz $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG18/F/.
cp $RawDatDir/FoxysporumPG18_S4_L001_R2_001.fastq.gz $ProjectDir/raw_dna/paired/F.oxysporum_fsp_pisi/PG18/R/.I also made new directories for FOP1, FOP2 and FOP5 and copied over the data (by being in the folder I wanted the data to be in, and changing the FOP number and file for each)
scp /home/groups/harrisonlab/project_files/fusarium/raw_dna/paired/F.oxysporum_fsp_pisi/FOP5/F/FOP5_S2_L001_R1_001.fastq.gz .#Data qc
programs: fastqc fastq-mcf kmc
Data quality was visualised using fastqc:
for RawData in $(ls raw_dna/paired/*/*/*/*.fastq.gz); do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/dna_qc
echo $RawData;
qsub $ProgDir/run_fastqc.sh $RawData
doneThe output for this is into the same location that the raw file came from, so e.g. raw_dna/paired/F.oxysporum_fsp_pisi/PG3/R. A new directory should appear in F/R directories for each isolate.
Can visualise this by navigating to the file in finder (after cluster mount on a new tab in terminal) and opening the html file in the browser.
##Data Trimming
Trimming was performed on data to trim adapters from sequences and remove poor quality data. This was done with fastq-mcf
for StrainPath in $(ls -d raw_dna/paired/*/*); do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/rna_qc
IlluminaAdapters=/home/jenkis/git_repos/tools/seq_tools/ncbi_adapters.fa
ReadsF=$(ls $StrainPath/F/*.fastq*)
ReadsR=$(ls $StrainPath/R/*.fastq*)
echo $ReadsF
echo $ReadsR
qsub $ProgDir/rna_qc_fastq-mcf.sh $ReadsF $ReadsR $IlluminaAdapters DNA
doneThis trims off the adapters from the fastq.gz file in raw_dna/paired/FOP1/F etc directories
Fastqc was performed again to visualise the quality of the data following trimming (using the same script as before):
Data quality was visualised once again following trimming: (with the same fast qc programme as before)
for RawData in qc_dna/paired/*/*/*/*.fq.gz; do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/dna_qc
echo $RawData;
qsub $ProgDir/run_fastqc.sh $RawData
done##kmer counting was performed using kmc. This allowed estimation of sequencing depth and total genome size:
for TrimPath in qc_dna/paired/*/*; do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/dna_qc
TrimF=$(ls $TrimPath/F/*.fq.gz)
TrimR=$(ls $TrimPath/R/*.fq.gz)
echo $TrimF
echo $TrimR
qsub $ProgDir/kmc_kmer_counting.sh $TrimF $TrimR
doneScript ran- not sure where the estimated coverage and genome size comes from?
#Assembly Assembly was performed using: SPAdes
A range of hash lengths were used and the best assembly selected for subsequent analysis
for StrainPath in $(ls -d qc_dna/paired/*/*); do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/spades
Strain=$(echo $StrainPath | rev | cut -f1 -d '/' | rev)
Organism=$(echo $StrainPath | rev | cut -f2 -d '/' | rev)
F_Read=$(ls $StrainPath/F/*.fq.gz)
R_Read=$(ls $StrainPath/R/*.fq.gz)
OutDir=assembly/spades/$Organism/$Strain
echo $F_Read
echo $R_Read
qsub $ProgDir/submit_SPAdes.sh $F_Read $R_Read $OutDir correct 10
doneAssembly stats can be visualised after running Quast.
But first you need to remove contaminants and change the headers to contigs.
#Removing contaminants- changing headers to contigs
This changes headers from Nodes to contigs in the fasta file and renames the file.
for OutDir in $(ls -d assembly/spades/*/*/filtered_contigs); do
ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/remove_contaminants
AssFiltered=$OutDir/contigs_min_500bp.fasta
AssRenamed=$OutDir/contigs_min_500bp_renamed.fasta
echo $AssFiltered
printf '.\t.\t.\t.\n' > editfile.tab
$ProgDir/remove_contaminants.py --inp $AssFiltered --out $AssRenamed --coord_file editfile.tab
rm editfile.tab
done#Quast
Tools used to summarise assembly statistics- to do with submission of genome to NCBI.
ProgDir=/home/jenkis/git_repos/tools/seq_tools/assemblers/assembly_qc/quast
for Assembly in $(ls assembly/spades/*/*/filtered_contigs/*_500bp_renamed.fasta); do
Strain=$(echo $Assembly | rev | cut -d '/' -f3 | rev)
Organism=$(echo $Assembly | rev | cut -d '/' -f4 | rev)
OutDir=assembly/spades/$Organism/$Strain/filtered_contigs
qsub $ProgDir/sub_quast.sh $Assembly $OutDir
doneFor future reference these report stats can be found in e.g. less assembly/spades/F.oxysporum_fsp_pisi/PG18/filtered_contigs/report.txt
Can note down assembly stats in an Excel file or txt file.
Repeat masking was performed and used the following programs: Repeatmasker Repeatmodeler
The best assembly was used to perform repeatmasking
ProgDir=/home/adamst/git_repos/tools/seq_tools/repeat_masking
for BestAss in $(ls assembly/spades/*/*/filtered_contigs/*_500bp_renamed.fasta); do
echo $BestAss
qsub $ProgDir/rep_modeling.sh $BestAss
qsub $ProgDir/transposonPSI.sh $BestAss
doneTakes like 24 hours
The number of bases masked by transposonPSI and Repeatmasker were summarised using the following commands:
for RepDir in $(ls -d repeat_masked/F.oxysporum_fsp_pisi/*/filtered_contigs_repmask); do
Strain=$(echo $RepDir | rev | cut -f2 -d '/' | rev)
Organism=$(echo $RepDir | rev | cut -f3 -d '/' | rev)
RepMaskGff=$(ls $RepDir/*_contigs_hardmasked.gff)
TransPSIGff=$(ls $RepDir/*_contigs_unmasked.fa.TPSI.allHits.chains.gff3)
printf "$Organism\t$Strain\n"
printf "The number of bases masked by RepeatMasker:\t"
sortBed -i $RepMaskGff | bedtools merge | awk -F'\t' 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}'
printf "The number of bases masked by TransposonPSI:\t"
sortBed -i $TransPSIGff | bedtools merge | awk -F'\t' 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}'
printf "The total number of masked bases are:\t"
cat $RepMaskGff $TransPSIGff | sortBed | bedtools merge | awk -F'\t' 'BEGIN{SUM=0}{ SUM+=$3-$2 }END{print SUM}'
echo
doneResults for ^ :
F.oxysporum_fsp_pisi FOP1 The number of bases masked by RepeatMasker: 8091753 The number of bases masked by TransposonPSI: 2341584 The total number of masked bases are: 8415943
F.oxysporum_fsp_pisi FOP2 The number of bases masked by RepeatMasker: 4710956 The number of bases masked by TransposonPSI: 1485557 The total number of masked bases are: 4972874
F.oxysporum_fsp_pisi FOP5 The number of bases masked by RepeatMasker: 3841697 The number of bases masked by TransposonPSI: 1313995 The total number of masked bases are: 4180881
F.oxysporum_fsp_pisi PG18 The number of bases masked by RepeatMasker: 5247951 The number of bases masked by TransposonPSI: 1627744 The total number of masked bases are: 5575676
F.oxysporum_fsp_pisi PG3 The number of bases masked by RepeatMasker: 4898473 The number of bases masked by TransposonPSI: 1680264 The total number of masked bases are: 5170668
#Gene Prediction
##Pre-gene Prediction - CEGMA
Pre-gene prediction - Quality of genome assemblies were assessed using Cegma to see how many core eukaryotic genes can be identified- looks for gene space.
for Assembly in $(ls assembly/spades/*/*/filtered_contigs/*_500bp_renamed.fasta); do
ProgDir=/home/jenkis/git_repos/tools/gene_prediction/cegma
qsub $ProgDir/sub_cegma.sh $Assembly dna
doneResults can be found in: e.g/ less gene_pred/cegma/fusarium_ex_pea/PG18/ Look for the in completeness report
Output were summarised using the commands:
for File in $(ls gene_pred/cegma/*/*/*_dna_cegma.completeness_report); do
Strain=$(echo $File | rev | cut -f2 -d '/' | rev);
Species=$(echo $File | rev | cut -f3 -d '/' | rev);
printf "$Species\t$Strain\n";
cat $File | head -n18 | tail -n+4;printf "\n";
done > gene_pred/cegma/cegma_results_dna_summary.txtTo view:
less gene_pred/cegma/cegma_results_dna_summary.txt
F.oxysporum_fsp_pisi FOP1 #Prots %Completeness - #Total Average %Ortho
Complete 238 95.97 - 282 1.18 11.76
Group 1 61 92.42 - 71 1.16 11.48 Group 2 54 96.43 - 62 1.15 11.11 Group 3 58 95.08 - 75 1.29 15.52 Group 4 65 100.00 - 74 1.14 9.23
Partial 243 97.98 - 297 1.22 14.81
Group 1 64 96.97 - 74 1.16 10.94 Group 2 55 98.21 - 65 1.18 14.55 Group 3 59 96.72 - 81 1.37 23.73 Group 4 65 100.00 - 77 1.18 10.77
F.oxysporum_fsp_pisi FOP2 #Prots %Completeness - #Total Average %Ortho
Complete 236 95.16 - 283 1.20 11.86
Group 1 60 90.91 - 71 1.18 11.67 Group 2 53 94.64 - 61 1.15 7.55 Group 3 58 95.08 - 79 1.36 20.69 Group 4 65 100.00 - 72 1.11 7.69
Partial 241 97.18 - 294 1.22 13.28
Group 1 63 95.45 - 75 1.19 11.11 Group 2 54 96.43 - 64 1.19 11.11 Group 3 59 96.72 - 80 1.36 20.34 Group 4 65 100.00 - 75 1.15 10.77
F.oxysporum_fsp_pisi FOP5 #Prots %Completeness - #Total Average %Ortho
Complete 241 97.18 - 277 1.15 10.37
Group 1 62 93.94 - 74 1.19 11.29 Group 2 54 96.43 - 59 1.09 7.41 Group 3 61 100.00 - 76 1.25 16.39 Group 4 64 98.46 - 68 1.06 6.25
Partial 244 98.39 - 290 1.19 12.70
Group 1 64 96.97 - 76 1.19 10.94 Group 2 55 98.21 - 62 1.13 10.91 Group 3 61 100.00 - 81 1.33 21.31 Group 4 64 98.46 - 71 1.11 7.81
F.oxysporum_fsp_pisi PG18 #Prots %Completeness - #Total Average %Ortho
Complete 242 97.58 - 295 1.22 15.70
Group 1 62 93.94 - 75 1.21 12.90 Group 2 54 96.43 - 63 1.17 12.96 Group 3 61 100.00 - 79 1.30 22.95 Group 4 65 100.00 - 78 1.20 13.85
Partial 246 99.19 - 311 1.26 18.70
Group 1 65 98.48 - 79 1.22 12.31 Group 2 55 98.21 - 67 1.22 18.18 Group 3 61 100.00 - 81 1.33 24.59 Group 4 65 100.00 - 84 1.29 20.00
F.oxysporum_fsp_pisi PG3 #Prots %Completeness - #Total Average %Ortho
Complete 241 97.18 - 288 1.20 12.86
Group 1 62 93.94 - 73 1.18 12.90 Group 2 54 96.43 - 63 1.17 14.81 Group 3 60 98.36 - 81 1.35 18.33 Group 4 65 100.00 - 71 1.09 6.15
Partial 245 98.79 - 300 1.22 15.10
Group 1 65 98.48 - 76 1.17 12.31 Group 2 55 98.21 - 66 1.20 18.18 Group 3 60 98.36 - 85 1.42 21.67 Group 4 65 100.00 - 73 1.12 9.23
##Gene prediction 1 - Braker1 gene model training and prediction (taken/adapted from the Fusarium repos) Gene prediction was performed using Braker1.
First, RNAseq data was aligned to Fusarium genomes.
qc of RNA seq data is detailed below:
for Folder in $(ls -d ../fusarium/raw_rna/paired/F.oxysporum_fsp_cepae/*); do
FolderName=$(echo $Folder | rev | cut -f1 -d '/' | rev);
echo $FolderName;
ls $Folder/F;
ls $Folder/R;
doneResults here for ^ commands:
55_72hrs_rep1 sample013_1.combined.fastq.gz sample013_2.combined.fastq.gz 55_72hrs_rep2 sample014_1.combined.fastq.gz sample014_2.combined.fastq.gz 55_72hrs_rep3 sample015_1.combined.fastq.gz sample015_2.combined.fastq.gz control_72hrs_rep1 sample002_1.combined.fastq.gz sample002_2.combined.fastq.gz control_72hrs_rep2 sample004_1.combined.fastq.gz sample004_2.combined.fastq.gz control_72hrs_rep3 sample005_1.combined.fastq.gz sample005_2.combined.fastq.gz FO47_72hrs_rep1 sample006_1.combined.fastq.gz sample006_2.combined.fastq.gz FO47_72hrs_rep2 sample007_1.combined.fastq.gz sample007_2.combined.fastq.gz FO47_72hrs_rep3 sample012_1.combined.fastq.gz sample012_2.combined.fastq.gz Fus2_0hrs_prelim 1_S1_L001_R1_001.fastq.gz 1_S1_L001_R2_001.fastq.gz Fus2_16hrs_prelim 3_S2_L001_R1_001.fastq.gz 3_S2_L001_R2_001.fastq.gz Fus2_24hrs_prelim_rep1 4_S3_L001_R1_001.fastq.gz 4_S3_L001_R2_001.fastq.gz Fus2_24hrs_prelim_rep2 Fus2_36hrs_prelim 36hr-root_S10_L001_R1_001.fastq.gz 36hr-root_S10_L001_R2_001.fastq.gz Fus2_48hrs_prelim 6_S4_L001_R1_001.fastq.gz 6_S4_L001_R2_001.fastq.gz Fus2_4hrs_prelim 4hr-root_S7_L001_R1_001.fastq.gz 4hr-root_S7_L001_R2_001.fastq.gz Fus2_72hrs_prelim 7_S5_L001_R1_001.fastq.gz 7_S5_L001_R2_001.fastq.gz Fus2_72hrs_rep1 sample016_1.combined.fastq.gz sample016_2.combined.fastq.gz Fus2_72hrs_rep2 sample018_1.combined.fastq.gz sample018_2.combined.fastq.gz Fus2_72hrs_rep3 sample019_1.combined.fastq.gz sample019_2.combined.fastq.gz Fus2_8hrs_prelim 8hr-root_S8_L001_R1_001.fastq.gz 8hr-root_S8_L001_R2_001.fastq.gz Fus2_96hrs_prelim 8_S6_L001_R1_001.fastq.gz 8_S6_L001_R2_001.fastq.gz Fus2_CzapekDox 6_S2_L001_R1_001_fastqc 6_S2_L001_R1_001.fastq.gz 6_S2_L001_R2_001_fastqc 6_S2_L001_R2_001.fastq.gz Fus2_GlucosePeptone 7_S3_L001_R1_001_fastqc 7_S3_L001_R1_001.fastq.gz 7_S3_L001_R2_001_fastqc 7_S3_L001_R2_001.fastq.gz Fus2_PDA 9_S4_L001_R1_001_fastqc 9_S4_L001_R1_001.fastq.gz 9_S4_L001_R2_001_fastqc 9_S4_L001_R2_001.fastq.gz Fus2_PDB 4_S1_L001_R1_001_fastqc 4_S1_L001_R1_001.fastq.gz 4_S1_L001_R2_001_fastqc 4_S1_L001_R2_001.fastq.gz
... if doing this with my own RNAseq data there would be additional steps here between these 2 commands.
Then Rnaseq data was aligned to each genome assembly:
for Assembly in $(ls repeat_masked/*/FOP5/*/*_contigs_unmasked.fa); do
Strain=$(echo $Assembly| rev | cut -d '/' -f3 | rev)
Organism=$(echo $Assembly | rev | cut -d '/' -f4 | rev)
echo "$Organism - $Strain"
for RNADir in $(ls -d ../fusarium/qc_rna/paired/F.oxysporum_fsp_cepae/*); do
Timepoint=$(echo $RNADir | rev | cut -f1 -d '/' | rev)
echo "$Timepoint"
FileF=$(ls $RNADir/F/*_trim.fq.gz)
FileR=$(ls $RNADir/R/*_trim.fq.gz)
OutDir=alignment/$Organism/$Strain/$Timepoint
InsertGap='-20'
InsertStdDev='78'
Jobs=$(qstat | grep 'tophat' | grep 'qw' | wc -l)
while [ $Jobs -gt 1 ]; do
sleep 10
printf "."
Jobs=$(qstat | grep 'tophat' | grep 'qw' | wc -l)
done
printf "\n"
ProgDir=/home/jenkis/git_repos/tools/seq_tools/RNAseq
qsub $ProgDir/tophat_alignment.sh $Assembly $FileF $FileR $OutDir $InsertGap $InsertStdDev
done
doneran again without: (as it stopped running when I quit terminal)
Jobs=$(qstat | grep 'tophat' | grep 'qw' | wc -l)
while [
Re-ran again as was getting an error message in the next section
F.oxysporum_fsp_pisi - FOP5 open: No such file or directory [bam_merge_core] fail to open file alignment/F.oxysporum_fsp_pisi/FOP5/55_72hrs_rep3/accepted_hits.bam Your job 6666661 ("sub_braker_fungi.sh") has been submitted
So ran again for FOP5, PG18 and PG3 separately 16.11.16
#Dont do again Up until now we have been using just the repeatmasker/repeatmodeller fasta file when we have used softmasked fasta files. You can merge in transposonPSI masked sites using the following command:
for File in $(ls repeat_masked/*/*/filtered_contigs_repmask/*_contigs_softmasked.fa); do
OutDir=$(dirname $File)
TPSI=$(ls $OutDir/*_contigs_unmasked.fa.TPSI.allHits.chains.gff3)
OutFile=$(echo $File | sed 's/_contigs_softmasked.fa/_contigs_softmasked_repeatmasker_TPSI_appended.fa/g')
bedtools maskfasta -soft -fi $File -bed $TPSI -fo $OutFile
echo "$OutFile"
echo "Number of masked bases:"
cat $OutFile | grep -v '>' | tr -d '\n' | awk '{print $0, gsub("[a-z]", ".")}' | cut -f2 -d ' '
done
repeat_masked/F.oxysporum_fsp_pisi/FOP1/filtered_contigs_repmask/FOP1_contigs_softmasked_repeatmasker_TPSI_appended.fa
Number of masked bases:
8415943
repeat_masked/F.oxysporum_fsp_pisi/FOP2/filtered_contigs_repmask/FOP2_contigs_softmasked_repeatmasker_TPSI_appended.fa
Number of masked bases:
4972874
repeat_masked/F.oxysporum_fsp_pisi/FOP5/filtered_contigs_repmask/FOP5_contigs_softmasked_repeatmasker_TPSI_appended.fa
Number of masked bases:
4180881
repeat_masked/F.oxysporum_fsp_pisi/PG18/filtered_contigs_repmask/PG18_contigs_softmasked_repeatmasker_TPSI_appended.fa
Number of masked bases:
5575676
repeat_masked/F.oxysporum_fsp_pisi/PG3/filtered_contigs_repmask/PG3_contigs_softmasked_repeatmasker_TPSI_appended.fa
Number of masked bases:
5170668
##Continue
#Braker prediction
Before braker predictiction was performed, I double checked that I had the genemark key in my user area and copied it over from the genemark install directory:
```bash
ls ~/.gm_key
cp /home/armita/prog/genemark/gm_key_64 ~/.gm_keyfor Assembly in $(ls repeat_masked/*/*/*/*_contigs_softmasked_repeatmasker_TPSI_appended.fa); do
printf "\n"
Strain=$(echo $Assembly| rev | cut -d '/' -f3 | rev)
Organism=$(echo $Assembly | rev | cut -d '/' -f4 | rev)
echo "$Organism - $Strain"
mkdir -p alignment/$Organism/$Strain/concatenated
samtools merge -f alignment/$Organism/$Strain/concatenated/concatenated.bam \
alignment/$Organism/$Strain/55_72hrs_rep1/accepted_hits.bam \
alignment/$Organism/$Strain/55_72hrs_rep2/accepted_hits.bam \
alignment/$Organism/$Strain/55_72hrs_rep3/accepted_hits.bam \
alignment/$Organism/$Strain/FO47_72hrs_rep1/accepted_hits.bam \
alignment/$Organism/$Strain/FO47_72hrs_rep2/accepted_hits.bam \
alignment/$Organism/$Strain/FO47_72hrs_rep3/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_0hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_16hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_24hrs_prelim_rep1/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_36hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_48hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_4hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_72hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_72hrs_rep1/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_72hrs_rep2/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_72hrs_rep3/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_8hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_96hrs_prelim/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_CzapekDox/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_GlucosePeptone/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_PDA/accepted_hits.bam \
alignment/$Organism/$Strain/Fus2_PDB/accepted_hits.bam
OutDir=gene_pred/braker/$Organism/"$Strain"_braker
AcceptedHits=alignment/$Organism/$Strain/concatenated/concatenated.bam
GeneModelName="$Organism"_"$Strain"_braker
ProgDir=/home/jenkis/git_repos/tools/gene_prediction/braker1
qsub $ProgDir/sub_braker_fungi.sh $Assembly $OutDir $AcceptedHits $GeneModelName
doneF.oxysporum_fsp_pisi - FOP1 Your job 6666565 ("sub_braker_fungi.sh") has been submitted
F.oxysporum_fsp_pisi - FOP2 Your job 6666660 ("sub_braker_fungi.sh") has been submitted
F.oxysporum_fsp_pisi - FOP5 open: No such file or directory [bam_merge_core] fail to open file alignment/F.oxysporum_fsp_pisi/FOP5/55_72hrs_rep3/accepted_hits.bam Your job 6666661 ("sub_braker_fungi.sh") has been submitted
F.oxysporum_fsp_pisi - PG18 open: No such file or directory [bam_merge_core] fail to open file alignment/F.oxysporum_fsp_pisi/PG18/FO47_72hrs_rep1/accepted_hits.bam Your job 6666662 ("sub_braker_fungi.sh") has been submitted
F.oxysporum_fsp_pisi - PG3 open: No such file or directory [bam_merge_core] fail to open file alignment/F.oxysporum_fsp_pisi/PG3/55_72hrs_rep3/accepted_hits.bam Your job 6666663 ("sub_braker_fungi.sh") has been submitted jenkis@bio72:/home/groups/harrisonlab/project_files/fusarium_ex_pea$
........................................................................................... NOTES FROM SKYPE
for the gene pred bit:
when you get here:
for Folder in
Do this:
for Folder in
To prevent copying over too much info. It will use Andrews folder instead.
ignore all commands between the above commands and: ‘Then Rnaseq data was aligned to each genome assembly:’ (qc and estimating insert size of reads - dont need any of this) Need command below this line ^ use initiative when running these- they will need adapting e.g grep -w "FUS2' (filters something out) I would not use this line as im not doing FUS2
the following command (in the last script after Then Rnaseq..) has the line: for RNADir in $(ls -d qc_rna/paired/F.oxysporum_fsp_cepae/* | grep -v -e '_rep'); do
again, you want to use the rnaseq data in my folder, so change this to: for RNADir in $(ls -d ../fusarium/qc_rna/paired/F.oxysporum_fsp_cepae/* | grep -v -e '_rep'); do
alignig RNAseq to data
From here the commands will be similar- they submit the braker job using the bam file you have just merged together (see 46mins)
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