I'm about to take delivery of large numbers of unmapped (demultiplexed) BAM files from a BGI sequencer with pairs of reads in the following form:
A1 77 * 0 0 * * 0 0 <sequence> <quality> RG:Z:rL1 RX:Z:GCGCCCC QX:Z:B(,:.)' BC:Z:GTCTAAACAG QT:Z:.',(/-+*;&
A1 141 * 0 0 * * 0 0 <sequence> <quality> RG:Z:rL1 RX:Z:GCGCCCC QX:Z:B(,:.)' BC:Z:GTCTAAACAG QT:Z:.',(/-+*;&
The barcodes (BC:/QT:) and the unique molecular indices (RX:/QX:) have already been removed from the reads and deposited in the relevant fields of the BAM file.
I need to process this into FASTQ format for the paired ends (flags 77 and 141 for a mate pair) to eventually use UMI-tools on the mapped data.
Is there a script anywhere that will take an unmapped BAM file in this format and turn it into a FASTQ of the format required to map before deduplicating through UMI-tools? I can brew my own, but if there's an off-the-shelf solution I could use, then I'd be grateful.
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Is this 10x data?
I'm not aware that it is, just that it will be in the above form - that is taken from an initial run with some known other samples so I can get familiarised with the format and develop pipelines before it arrives.
graeme, do you have a policy of not following up on your previous threads? - How do I download TCGA SNV data for patients with ER+/HER2- breast cancer?
It would be the courteous thing to do.
Sorry, just replied to that and accepted your answer.
If you can find a mapper that will handle the unmapped BAM as input, UMI-tools is more than happy to take the library barcodes and UMI sequences from a BAM tag, rather then the read name.
Thanks, just spotted those options --umi-tag and --extract-umi-method=tag. STAR can use unmapped BAM files as input and (according to its docs) retains all tags when mapping so it can be used prior to that. Now just to find a solution to clip/trim the unmapped BAM before trying to align.
STAR should soft clip during alignment.