Zero-length fragments generated from Cell Ranger BAM
cflerin opened this issue · comments
Hi, thanks for making this tool!
I've come across this issue and I'm not sure if this is the expected behavior or not. I'm using Sinto 0.7.1
to create a fragments file from a Cell Ranger bam file. In the output, I get many fragments with the same start/end position (around 6000 in total). For example:
chr5 49658161 49658162 CGCACAGCACCTATTT-1 1
chr5 49658161 49658164 GATTGACCACGTTGTA-1 2
chr5 49658161 49658168 TGTGTCCGTATTGTCG-1 1
chr5 49658162 49658162 CTCTACGCAAAGGTCG-1 1 # <--- this fragment
chr5 49658162 49658168 CCGTACTCACACACAT-1 2
chr5 49658162 49658173 GTGGATTCAGCAACAG-1 1
chr5 49658166 49658432 CTGAATGAGGACTAGC-1 2
chr5 49658168 49658168 CACCTTGAGCCTGTAT-1 3
When comparing to the Cell Ranger fragments file from the same bam, I don't see any of these. From Cell Ranger, the minimum fragment size seems to be 10, so maybe it has been filtered. Should I filter the Sinto fragments as well?
Hi, I think filtering fragments based on a minimum length is definitely a good idea, I hadn't noticed any of these very short fragments in the test cases I looked at. I can add a minimum fragment length argument to the next version, similar to how we have the --max_distance
parameter
Hi @timoast, thanks for the reply. For now, I can work around this by just filtering for a minimum fragment size during the filtering step:
sort -k1,1 -k2,2n fragments.bed | awk '($3-$2) >= 10' | bgzip -c > fragments.tsv.gz
So, feel free to close this, unless you're planning on adding the filtering step in a later release.
I'll leave this open until an option is added to sinto to filter small fragments
Now added in 0.7.2