Question: Error when putting multiple read files in CITE-seq-Count
0
gravatar for yhuang690
8 months ago by
yhuang6900
yhuang6900 wrote:

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
ADD COMMENTlink modified 8 months ago by genomax78k • written 8 months ago by yhuang6900

"CITE-seq-Count: error: unrecognized arguments:"

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 cat them prior to feeding them into CITE-seq-count.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax78k

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.

ADD REPLYlink written 8 months ago by yhuang6900

Sequence length in L001_R2.fastq.gz is not consistent.

CITE-seq may require untrimmed original data. Perhaps your reads have already been trimmed?

I thought CITE-Seq-Count should be able to intake multiple input files.

That does not seem to be the case based on quick glance at the online manual page.

ADD REPLYlink written 8 months ago by genomax78k

The data I'm using is untrimmed.

ADD REPLYlink written 8 months ago by yhuang6900

Hi! Did you ever find the solution to this?

Thanks!

ADD REPLYlink written 3 months ago by akornberg50
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