ERROR kallisto: unrecognized option `--kmer about kb_python HOT 6 CLOSED

Hi, @khushboojindal,
I notice that you are providing three FASTQ files as input, while the 10xv3 technology requires two, where the first contains the biological cDNA reads and the second contains the reads with the barcode and UMI sequences.

Based on the filenames for the three FASTQs, I suspect you can just provide the R1.fastq.gz and R2.fastq.gz files (and omit the I1.fastq.gz.

As for the --kmer option, could you let me know what version of kb you are using? You can check this by just running kb without any arguments.

from kb_python.

Hi @Lioscro ,

Thanks for your response.

R1.fastq.gz , R2.fastq.gz and L1.fastq.gz are from the same sample but loaded in different lanes in 10x. Is there a way to load all three or not sure if we can skip L1 here:/

Kb version:

(base) khushbl@BK-MAC ~ % kb info
kb_python 0.25.1
kallisto: 0.46.2
bustools: 0.40.0

from kb_python.

Does your third FASTQ start with an I or an L? I ask this because Illumina sequencers always output a third index sequence FASTQ that contains an I instead of R.

Could you post the first few reads from each file? You can do so with the following command.

gunzip -c R1.fastq.gz | head -n 12

and the analogous for the other two files.

from kb_python.

Thanks for your prompt response!

Yes, The third file start with I .

R1.fastq.gz

@NB502117:158:HJ337BGX7:1:11101:2571:1040 1:N:0:GTTCCTCA
AGGTCNGCACGCTTTCCGCCAGATGT
+
AAAAA#EEAEEEEAEEEEEEEEE/AA
@NB502117:158:HJ337BGX7:1:11101:14979:1040 1:N:0:GTTCCTCA
CCATTNGTCACATACGGTCTACTTCG
+
AAAAA#EEEEEEEEEEEEEEEEEEEE
@NB502117:158:HJ337BGX7:1:11101:7745:1040 1:N:0:GTTCCTCA
AAGGTNCAGTGGTAATCCCGTAGACG
+
AAAAA#EEEEEEEEEEEEEEEEEEE<

R2.fastq.gz

@NB502117:158:HJ337BGX7:2:11101:4877:1040 2:N:0:GTTCCTCA
CTACACACCTTATCCCCATACNAGTTATTATCGAAACAATCANCCTACTNNTTCANNNNNTAGCCCTNGNCGTACNCCTAACNGCTAACATTACTGAA
+
AAAAA///EEEA//AEEEEEE#AEA/EEEEE/EAE/A/6/EE#//EE/E##EE/E#####EEEEEEE#/#//EE<#</E<EE#/EE/E<AEEEAE//A
@NB502117:158:HJ337BGX7:2:11101:17921:1040 2:N:0:GTTCCTCA
GGGGGGGGGGGGGGGGGGGGGNGGGGGGGGGGGGGGGGGGGGNGGGGGGNNAAGTNNNNNTGTTTTTNTNATTTANTATTTTNATTAATAATAAAAAA
+
AAAAAEEEEEEEEEEEAAAEE#EEEEA66666///6666/6/#//////##////#####///////#/#/////#//////#///////////////
@NB502117:158:HJ337BGX7:2:11101:8646:1040 2:N:0:GTTCCTCA
GTAAAAGCAGTCCTACTCTTCNACACTAGGAAGGCTTTACTTNTTTTAANTGGTGNAGNNGGAAAATNGNACATTNCATACTNAATTGGGTCCTTGTC
+
AAAAAEEEEEEEEEEEEEEEE#EEEEEEEEEAEEEEEEEAEE#EEEEEE#EEEEE#EE##EEEAEEE#/#EEEEE#/EEEEE#EEEEAEEEEEEEEE<

I1.fastq.gz

@NB502117:158:HJ337BGX7:1:11101:2571:1040 1:N:0:GTTCCTCA
GTTCCTCA
+
AAAAAEEE
@NB502117:158:HJ337BGX7:1:11101:14979:1040 1:N:0:GTTCCTCA
GTTCCTCA
+
AAAAAEEE
@NB502117:158:HJ337BGX7:1:11101:7745:1040 1:N:0:GTTCCTCA
GTTCCTCA
+
AAAAAEEE

from kb_python.

Hi, @khushboojindal,
Thanks for looking into that.
I believe the I1.fastq.gz is the Illumina index read that should not be input into kb.
Could you try re-running kb without this file and let me know if you experience any other problems?

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