Closed cflerin closed 3 years ago
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
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: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?