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
Is there anything in the log file?
I don't even get a log file as an output, which just adds to my confusion
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?