VGP/vgp-assembly

10X align

zhoudreames opened this issue · 3 comments

zhoudreames commented

in your pipeline,the longrange software using fixed fastq format in blow：
_S*_L00*_R1_001.fastq.gz
_S*_L00*_R2_001.fastq.gz
if the 10x fastq data trim barcode or not ？

I got the average molecule coverage is 234 when I aligned 10X data by using longrange,but the mean depth only is 89 .I dont know what means the average molecule coverage, and is the value reasonable？

Arkarachai commented

I can answer the first part. For longranger step, the 10x is not trimmed.

arangrhie commented

Hi @zhoudreames, yes, the 10x fastq data contain the barcode info.
The molecule coverage in asset are inferred from these barcodes, which is different from the physical coverage of the reads.
Reads containing same barcodes within certain length are considered as one molecule, which could contain physical coverage gaps.

  • 👍2
zhoudreames commented

Hi @zhoudreames, yes, the 10x fastq data contain the barcode info.
The molecule coverage in asset are inferred from these barcodes, which is different from the physical coverage of the reads.
Reads containing same barcodes within certain length are considered as one molecule, which could contain physical coverage gaps.

I can answer the first part. For longranger step, the 10x is not trimmed.

thank you so mush