Closed t-neumann closed 3 years ago
Very likely, all reads are removed due to very poor quality due to Sanger score ". Most likely, replacing all " with I, should fix this.
Yupp that fixed it - I checked and there are new base quality scores provided in the TCGA bams. So a samtools fastq
conversion automatically assigns the lowest score to them.
This parameter fixes it:
-v INT default quality score if not given in file [1]
so I used -v 40
.
Hi Daniel,
I get the following error for some TCGA RNA-seq datasets (
info.txt
):The read set itself looks good to me, is it maybe the missing quality scores?
Find also the read set I'm running (pre-filtered read set of oncogenes) below:
https://tinyurl.com/y4xj8vzo