This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Fastq-Dump And Bowtie Mapping

Hello,

if i create fastq files from .sra files using fastq-dump (default options), what quality is used in the fastq files and which options do i need to use with bowtie mapper? (default, --solexa-quals, etc.)?

Tnx, Gregor

fastq bowtie
• 4,959 views • link
updated by Darked89 Darked89 • written by Gregor Rot Gregor Rot

2 answers

Instead of downloading from SRA, use the same ID, search and download from EBI ENA archive in gziped fastq format, also using Aspera.

Compare:

http://www.ebi.ac.uk/ena/data/view/SRS074453

http://www.ncbi.nlm.nih.gov/sra?term=SRS074453

Reads are in phred quality scale.

• 1 views • link
written by Darked89 Darked89

Wonderful, EBI is making life easier for everybody.

• 0 views • link
written by Gregor Rot Gregor Rot

There is no requirement for specific quality type for submission to SRA. So files downloaded from SRA can have any of the possible quality score scales.

[?]Here[?] is a seqanswers thread on it. You can use fastqc to check the quality score type, or try using that perl script in the thread.

• 0 views • link
written by Damian Kao Damian Kao

Log in to answer this question.

More posts like this