Conversion Of Solid Next Generation Sequencing Data

Question

[Anuraj Nayarisseri]

In next generation sequencing data are FASTQ format. In the case of Applied Biosystems SOLiD, next generation sequences may be represented by four digits - 0, 1, 2, and 3 followed by 'T'. how to handle paired-end sequencing data. Is there any conversion tool?? is there any tool can capable of handling paired-end sequencing data?

[Eric Normandeau]

Hi @Anuraj. Questions like this are highly pertinent for the forum! Please take some time to give more details, notably about what you are trying to accomplish. The more precise you explain your problem, the more helpful the answers will be for both you and all the other users. Cheers! :)

[Eric Normandeau]

Hi @Anuraj. Questions like this are highly pertinent for the forum! Please take some time to give more details, notably about what you are trying to accomplish. The more precisely you explain your problem, the more helpful the answers will be for both you and all the other users. Cheers! :)

Answer 1

[brentp]

BFast (and software here) handles colorspace reads well. As does bwa. It's better to use an aligner that supports colorspace, rather than converting to base space. See, for example, this.

[Aleksandr Levchuk]

+1 for comment on using the original vs. converting

Answer 2

[Aleksandr Levchuk]

The assembly/alignment tools Mosaik and MAQ both work with SOLiD data.

MAQ does it by using a converter. Please see solid2fastq.pl in the scripts folder.

Answer 3

[User 59]

Some tools, and you will need to check which, work with 'colourspace' data natively. For read mapping you may end up having to convert your reference sequences to colourspace however. Most tools will let you know if you can use colourspace reads natively.

Until you tell us what you need to do with the data, we can't help you much further. There are tools to convert csfasta data to fasta data for instance here. In fact you should probably familiarise yourself with solidsoftwaretools quite intimately if you're going to work with SOLiD data.

Answer 4

[Farhat]

I second Brent's idea on doing alignments in colorspace rather than converting to basespace. Here's how I work with colorspace data (the parameters should be changed for your data, these ones are quite screwy, check bowtie manual):

#convert colorspace to fastq to be able to use tools like FastQC
solid2fastq sample.csfasta sample.qual > sample.fastq

#create colorspace index
crossbow-1.1.0/bin/linux64/bowtie-build -f -C genome.fa genome

#create alignment
bowtie -C -5 3 -v 2 -l 20 --best -S -p 8 --minins 1900 --maxins 2100 -q -1 sample_F3.1.fastq -2 sample_R3.1.fastq genome | samtools view -bS - > sample.bam