What Better Way To Get The Paired Reads Aligned Against The Reference Genome?

Question

[thiagomafra]

Hi everybody,

I have a group of paired reads sequenced using Solid 4 (50bp each mate). I discovered that reads are contaminated by E.coli. My strategy is to align the reads against the reference genome and against the genomes of E.coli, and separate the aligned and no-aligned reads, respectively.

My question is: how to better way to get the paired reads, from the SAM file or during alignment? I use Shrimp, that allow to use the parameter --al (aligned reads) and --un (unaligned reads).

Help me?

Answer 1

[thiagomafra]

Other point: what better way by to separate the paired-reads?

I tried using awk in the fastq file generated during alignment with Shrimp, but the file contains reads of two mates; in the example below, the first two reads are F3 (T first base), but the third is R3 (G first base).

awk '0 == ((NR+4) % 8)*((NR+5) % 8)*((NR+6) % 8)*((NR+7) %8)' reads_infile.fastq > reads_R3.fastq 
awk '0 == (NR % 8)*((NR+1) % 8)*((NR+2) % 8)*((NR+3) %8)' reads_infile.fastq > reads_F3.fastq

@745_16_856
T02003003033333222200222111120220123212..012120..2.
+
&BB4BB<%B&%A+9<BB%-3':A%+A%9;;4>)%3A.?!!/2?)+:!!?!
@745_16_901
T00003012031232012222023200123133032010..202103..2.
+
=()%?0%B>-/A*'5@A7+=&%%7,%+%%'8@%*>,%8!!%9(&35!!-!
@745_16_918
G..20...211..032..1013.001..121..2.1..0213.021...11
+
!!?>!!!%AA!!=B8!!,?@%!3:@!!@,%!!5!1!!%.%?!-%0!!!<?

[Josh Herr]

Have you answered your question or are you just clarifying your question above? I can't tell and you are not clear. Please place clarifications in your original answer.

Answer 2

[Ian]

The only success i had with paired-end mapping on SOLiD4 was with BFAST+BWA. I could never get BFAST to map the F5 reads.

See also bwa mapping of solid paired end reads