Empty output from UMItools dedup after fastp processing
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11 months ago

Hello,

I have been running into an interesting error during my sequencing analysis.
We have a paired-end library with UMIs on both ends of the fragments, 6 nts each, for a total of 12 nt.
Now, I have been using fastp for preprocessing of my reads, including adapter and quality trimming, base correction, PolyG trimming and also UMI extraction. Here one exemplary command:

fastp -i sample1_R1.fastq -I sample_R2.fastq --umi --umi_loc=per_read --umi_len=6 --trim_poly_g 10 --html sample1_fastp.html -w 32 -c -o sample1_R1_fastp.fastq -O sample1_R2_fastp.fastq


After alignment (bowtie2) I wanted to use UMItools dedup on the .bam files, however then the resulting output .bam files are entirely empty. Here the command:

umi_tools dedup -I sample1.BAM --paired --umi-seperator=":" -S sample1_dedup.bam -L sample1_dedup.log


The seperator was of course specified, as fastp by default uses ":" as a seperator.

Has anyone run into a similar issue and if so, have you found a workaround?
I am thankful for any and all replies!

Cheers

deduplication fastp UMItools • 639 views
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Is there anything in the log file?

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I don't even get a log file as an output, which just adds to my confusion

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That is very werid. The file should at least be created, even if nothing goes into it. Can you run the same command without either the -S or the -L, this should send all output (both standard out and logging) to console. See if anything is output at all?