the usage of fastq-dump

Question

[yueli7]

Heloo,

I tried to use fastq-dump to split SRR file into three files: fastq, barcode+uMI and reads.

But the result only has one file.

Thanks in advance for any help!

Best,

Yue

/bin$ fastq-dump --gzip --split-3 --defline-qual '+' --defline-seq '@\$ac-\$si/\$ri'   SRR6956073.sra 
Read 161274652 spots for SRR6956073.sra
Written 161274652 spots for SRR6956073.sra
/bin$ alias fd='fastq-dump --split-3 --defline-qual '+' --defline-seq '@\\\$ac-\\\$si/\\\$ri' '

[yueli7]

10x chromium data will have cell/sample barcodes encoded in the BAM file. You can find that BAM file in "Data Access" tab in SRA record for this accession. Information you are looking for should be in CB and BC tags. Here is a full list of the tags for 10x BAM

[GenoMax]

This is not the answer for your question. I will remove the accepted toggle from it.

[yueli7]

Hello, genomax,

Thank you so much for your great help!

Best,

Yue

Answer 1

[GenoMax]

10x chromium data will have cell/sample barcodes encoded in the BAM file. You can find that BAM file in "Data Access" tab in SRA record for this accession. Information you are looking for should be in CB and BC tags. Here is a full list of the tags for 10x BAM.