Question: How to blast a paired end fastq file?
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gravatar for chillchik29
12 months ago by
chillchik290 wrote:

Hello everyone, I have a paired end fastq file and I know that BLAST+ in command line, accepts fasta format. But I don't know how does it work for a paired end fastq file (I mean in two different files R1 and R2). Do I have to interleave them and then convert them to fasta? Or should I concatenate them and convert them to fasta? Or should I treat them as separate files and then convert them to fasta?

Thank you, any help would be appreciated.

ADD COMMENTlink modified 12 months ago by chen2.0k • written 12 months ago by chillchik290
1

Why do you wish to BLAST read sequences? Plus, why do you want to BLAST both pairs and all reads?

ADD REPLYlink written 12 months ago by RamRS27k

I already selected these group of reads from all the metagenome sequences by aligning them with bbmap, to the phage_nt db. So before assembling them, I wanted to have a first approach of what I had in the sample by aligning them with BLAST and then export it to MEGAN.

ADD REPLYlink written 12 months ago by chillchik290
1

You could save some effort and only convert one end to fasta (reformat.sh in=R1.fq.gz out=R1.fa) and then BLAST. PE reads are not going to give you much additional information that MEGAN can use.

ADD REPLYlink written 12 months ago by genomax83k

Thank you! I'm going to try that out :)

ADD REPLYlink written 12 months ago by chillchik290
0
gravatar for JC
12 months ago by
JC10k
Mexico
JC10k wrote:

Use Magic-Blast

ADD COMMENTlink written 12 months ago by JC10k

While this would work to do the alignments it would produce SAM format output. I am not sure if MEGAN can use that.

ADD REPLYlink written 12 months ago by genomax83k
1

magic-blast also reports aligment in tabular format, which is similar to blast outfmt 6

ADD REPLYlink written 12 months ago by JC10k

Ah I missed that. It may need some manipulation (since it is not quite outfmt 6). I guess OP can let us know.

ADD REPLYlink written 12 months ago by genomax83k
0
gravatar for chen
12 months ago by
chen2.0k
OpenGene
chen2.0k wrote:

You can use fastp to merge it first, then blast the merged reads

See the intro here: https://github.com/OpenGene/fastp#merge-paired-end-reads

ADD COMMENTlink written 12 months ago by chen2.0k
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