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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Convert BAM files (Cell ranger) to SNAP files #134

Closed AitorAndueza closed 4 years ago

AitorAndueza commented 4 years ago

Hello,

I am new with bioinformatics and I am trying to convert Ban files generated with cell ranger into Snap file following these instructions: https://github.com/r3fang/SnapATAC/wiki/FAQs#cellranger_output

However, I have an issue in this step: $ samtools sort -n -@ 10 -m 1G atac_v1_adult_brain_fresh_5k_possorted.snap.bam -o atac_v1_adult_brain_fresh_5k.snap.nsrt.bam

In stead of generating just one snap.nsrt.bam file, it generates me 350 files, named from 1 to 350. Therefore, I don't know how to continue in the next step.

Can someone help me? I would really appreciate your help.

Best,

Aitor

yeswzc commented 4 years ago

It means the 'samtools sort' step had not finished. Wait till samtools finish the job, if failed try again.

AitorAndueza commented 4 years ago

Ok, I will tried again. Anyway, when the samtools sort function is running and generating this files, an error appear. It says that more symbols or letters are needed. Is it correct or it is weird?

yeswzc commented 4 years ago

I've never seen see before. Do you mind to give a screen shot of the reported error?

AitorAndueza commented 4 years ago

Thank you for your help. The error was solved updating the new Snaptools version. Thank you though.

r3fang commented 4 years ago

@yeswzc thanks for solving the issue!