is there any function to extract fastq for certain cells passing the filter?

Question

is there any function to extract fastq for certain cells passing the filter?

Opened this issue 7 years ago · 1 comments

Hi, I used umis cb_histogram to calculate reads count for each cell and then chose a count cutoff based on that. For the downstream analysis, such as pseudo-align and count UMI, we only need to deal with reads from those cells. Is there any function for this based on umis cb_histogram results? Thanks.

Answer 1 · 2017-10-11T14:06:53.000Z

Hi Xin,

Sorry for not responding sooner. There isn't functionality for the FASTQ file, but there is from an alignment file. umis subset_bamfile will subset a BAM file and keep only the given cellular barcodes.