tobiasrausch / atacseq Goto Github PK

Hi Trausch,

I wonder about one step (cut adapter step) in your pipeline. You set a specific "sequence" to remove the adapter, and I don't know whether this could affect the outcome (follow your pipeline). Is there any chance to take this step automatically or take our option?

This is a great pipeline (ALL in one)!

Thanks,
Haitao

For the motif/downloadMotifs.sh script,

curl --output jaspar.zip 'http://jaspar.genereg.net/download/CORE/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.zip'

It seems that the downloaded zip file is actually not a zip file. I manually downloaded the zip file and then the rest lines work.

Dear,
Thank you for this project for ATAC-Seq analyse.
I don't understand how Bowtie step could work, line 46 in align.sh:
bowtie2 --threads ${THREADS} --local --maxins 2000 -x ${HG} -1 ${OUTP}.1.fq.gz -2 ${OUTP}.2.fq.gz 2> ${OUTP}.bowtie.log | samtools view -bT ${HG} - > ${OUTP}.raw.bam

-x ${HG} requires a Bowtie index
-bT ${HG] requires a fasta file

So either I have a error of Bowtie2 ... does not exist or is not a Bowtie 2 index

So what should I indicate as <genome.fa> argument in atac.sh? Or should I indicate the Bowtie index in align.sh?

Best,

Hi Tobias,

I am following your ATACseq tutorial and am currently at step 2.9 (Annotate genomic context). I'm able to make the gr object from the data frame. However, when I try to use the annotatePeak function from Dr.Yu's ChIPseeker, I get the following error:

My code (from the tutorial):

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakAnno <- annotatePeak(gr, tssRegion=c(-1000, 1000), TxDb=txdb, annoDb="org.Hs.eg.db", verbose=TRUE)

Terminal Output:

preparing features information... 2021-12-08 03:28:04 PM
identifying nearest features... 2021-12-08 03:28:04 PM
Error in which(strand(subject) != "-") :
argument to 'which' is not logical

I interrogated strand(gr) for the sample dataset in your tutorial:
factor-Rle of length 57891 with 1 run
Lengths: 57891
Values : *
Levels(3): + - *

I wonder if the function is having trouble with the factor-Rle object. Are you able to help with this?

Many thanks,

George

HI ,
When I cd bed/ && Rscript promoter.R
I get this information in R
Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) :

Any help for this error will be appreciated!

Thanks!