Fastq-Dump And Bowtie Mapping

Question

[Gregor Rot]

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

Answer 1

[Darked89]

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.

[Gregor Rot]

Wonderful, EBI is making life easier for everybody.

Answer 2

[Damian Kao]

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.