Li Song
Li Song
The two-file barcoding system is not supported. You can use the command "paste -d'\0' bc1.fq bc2.fq > pasted.fq" to put the BC1, BC2, BC3 and BC4 into the same line...
Thanks for sharing your test results with us. Indeed, the length distribution change is too sharp, and the fragment length 0 should not happen either. Is the data publicly available?...
Thanks for sharing the data! We will look into this issue.
Hi @loraince, the fragment length 0 alignments seem to be chimeric reads or other sequencing artifacts. The example you mention should be the read: A00253:575:HWWVTDSX2:4:1260:28691:24314, where BWA-MEM aligned it on...
We just made an fix for the SAM format wich should resolve your issue of "Positional data too large". To pipe the output to samtools, you could specify the output...
For the multi-mapped reads, their mapq will be 0 and will be filtered out in Chromap's output by default (-q 30). So you can assume the alignments in Chromap's output...
It looks like this is the case. Is your data single-end? Or the genome is very repetitive?
I think you can try the option -q 1, so Chromap can output more reads.
Based on the two lines: Number of barcodes in whitelist: 2890. Number of corrected barcodes: 41349117. It seems only a tiny fraction of reads' barcodes are in the whitelist. Could...
Yes. We should be more clear that Chromap will skip the reads whose barcodes are not in the whitelist, at least in the README. I think the line "Number of...