Question: Convert colorspace fastq to basespace fastq
0
gravatar for aflrios
6 months ago by
aflrios0
aflrios0 wrote:

Convert Solid color space fastq in base space fastq

Hi all I am a beginner in NGS. I downloaded some SRA files (from SRA-NCBI) and, I convert in ABI-solid fastq using fastq-dump. I would like to convert these ABI-solid files in Illumina fastq format. Does anyone know of any program that does this? Thank you. Álvaro.

rna-seq • 385 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by aflrios0
1

Your data may already be in fastq format, if you used fastq-dump. Can you show us the output of head -8 your.fq?

ADD REPLYlink written 6 months ago by genomax65k

Hi,

I would like to use this colorspace files for transcriptome assembly, but I think the softwares I am using (HISAT and StringieTie) work with base space files. So, I would like to convert colorspace to base space.

ADD REPLYlink written 6 months ago by aflrios0

Assuming that the data you need is not available on any other platform, you may want to use colorspace reads directly for the analysis. No need to convert the reads. You can use Tophat with bowtie1 option. Use bowtie version 0.12.7 or lower.

ADD REPLYlink modified 6 months ago • written 6 months ago by Satyajeet Khare1.3k

You can use Subjunc and then proceed with StringTie, it has been reported to work:

Whole RNA-Sequencing and Transcriptome Assembly of Candida albicans and Candida africana under Chlamydospore-Inducing Conditions

Question: Clarification of good pipeline for transcriptome assembly of RNA-seq data

I've updated my answer bellow to clarify why it is not a good idea to convert colorspace to basespace.

ADD REPLYlink written 6 months ago by h.mon24k
0
gravatar for h.mon
6 months ago by
h.mon24k
Brazil
h.mon24k wrote:

First, do you really need to work with those Solid reads? It is a defunct platform, with not much software available.

I would advise against converting colorspace to basespace, use a mapper / assembler that can take colorspace reads. For RNAseq, Subread and Subjunc (for spliced alignment) can map colorspace reads.

Due to how colorspace reads are encoded, if you convert a colorspace read with a sequencing error to basespace, the error causes a "frameshift" and all subsequent bases are also wrongly converted - this could affect adversely both mapping and (to a greater extent) de novo assembly. However, if you map in colorspace, sequencing errors can detected - as they can be differentiated from true SNPs - and corrected.

See better explanations at:

A: convert SOLID color space to base-space

http://seqanswers.com/forums/showpost.php?p=4977&postcount=2

ADD COMMENTlink modified 6 months ago • written 6 months ago by h.mon24k
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