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arshajii / ema

Fast & accurate alignment of barcoded short-reads
http://ema.csail.mit.edu
MIT License
32 stars 7 forks source link

10x bamtofastq with EMA BAM #23

Closed vladsavelyev closed 6 years ago

vladsavelyev commented 6 years ago

Hi,

A side feature request popped up while exploring the hg38 alignments peculiarities.

I tired to use this tool to convert a portion of EMA BAM file back to barcoded FASTQ: https://support.10xgenomics.com/docs/bamtofastq But the tool reported it as "Unrecognized 10x BAM file.". I guess it's likely that the tool is too tied to Lariat specificities. But it would be fantastic if EMA BAMs were compatible with this tool. Not sure if it's feasible without the modifications of the tool.

Or maybe there are alternatives that you could suggest?

Vlad

sjackman commented 6 years ago

I use samtools fastq -TBX to convert a BAM file with BX:Z tags to FASTQ with BX:Z tags.

vladsavelyev commented 6 years ago

Thanks Shaun, that should work I guess since EMA started to support BX:Z-tagged FASTQs

sjackman commented 6 years ago

No worries, Vlad. Happy to help.