Error when putting multiple read files in CITE-seq-Count
Hello,
I have 8 files for both read 1 and read 2 , while I put those files in read 1 and read 2 (8 total) into the script it throw out an error saying "CITE-seq-Count: error: unrecognized arguments:" . I think Cite-seq-count should be able to support multiple read files, right?
My command is
CITE-seq-Count: -R1 L1-R1.fastq.gz L2-R1.fastq.gz L3-R1.fastq.gz L4-R1-fastq.gz -R2 L1-R2,fastq.gz L2-R2.fastq.gz L3-R2.fastq.gz L4-R2.fastq.gz -t Antibodytag.csv -cbf 1 -cbl 16 -umif 17 -umil 26 -cells 6121 -o output
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colindaven
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yhuang690 •
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yhuang690 •
1 answer
This was discussed and solved here for future reference: https://github.com/Hoohm/CITE-seq-Count/issues/97
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Have you checked the inline help/manual for the program? You can't go beyond what kind of input the program expects.
I don't think using a
:in your command line is likely an acceptable input as well.Edit: Looking at the program manual it looks like the program only accepts a pair of files at a time. If those files represent lane specific ones then you can
catthem prior to feeding them intoCITE-seq-count.I have a typo at the answer, actually there is no ":" at my actual command, I tried to use "cat" to concatenate all the files but it throw out and error saying " Sequence length in L001_R2.fastq.gz is not consistent. Please, trim all sequences at the same length.". And I also reading some post online saying that better not just concatenate different lane files. I thought CITE-Seq-Count should be able to intake multiple input files.
CITE-seq may require untrimmed original data. Perhaps your reads have already been trimmed?
That does not seem to be the case based on quick glance at the online manual page.
The data I'm using is untrimmed.
Hi! Did you ever find the solution to this?
Thanks!