Questions tagged [read-correction]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
2 votes
1 answer

If fastp output is not a good measure of FASTQ correctness, what is?

In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment But I ...
gl00ten's user avatar
  • 249
0 votes
1 answer

Error when using awk command to trim sequence files

I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all ...
Justin1609's user avatar
2 votes
1 answer

Total read count of shotgun affected by few highly abundant sequences

I am building statistical models to analyse output from Illumina shotgun sequencing (HiSeq 4000) on stool samples (but RNA-seq data should behave similarily). The raw counts are a statistical sample ...
Rene's user avatar
  • 21
5 votes
1 answer

At what stage of a transcriptome assembly is it better to perform read contaminant filter?

I'm trying to assemble a bivalve transcriptome. Since bivalves are filter feeders, their transcriptomes tend to be highly contaminated by bacteria, algae and whatnot. Since I pooled several ...
LinuxBlanket's user avatar
2 votes
1 answer

How to force pilon to correct a reference with low coverage mapped reads?

I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I ...
conchoecia's user avatar
  • 3,141
2 votes
1 answer

Can I pilon-polish long reads with Illumina short reads to improve structural variant detection?

I have pacbio Sequel data at 50 x coverage for a strain of animal. I would like to find structural variants compared to the reference genome sequence. At the moment, I align my reads to the reference ...
Biomagician's user avatar
  • 2,459