Question: the usage of fastq-dump
0
gravatar for yueli7
13 months ago by
yueli7190
China
yueli7190 wrote:

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' '
rna-seq • 770 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by yueli7190
1

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

ADD REPLYlink modified 13 months ago • written 13 months ago by yueli7190

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

ADD REPLYlink written 13 months ago by GenoMax95k

Hello, genomax,

Thank you so much for your great help!

Best,

Yue

ADD REPLYlink written 13 months ago by yueli7190
4
gravatar for GenoMax
13 months ago by
GenoMax95k
United States
GenoMax95k wrote:

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.

ADD COMMENTlink modified 13 months ago • written 13 months ago by GenoMax95k
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