Bowtie1's --12 option in Bowtie2

[Tonnny97]

Hi all,

I would like to ask whether Bowtie2 can accept the .fastq in "1-read-per-line format (Tab-delimited format)"? (--12 option in Bowtie1)

Thanks for the reply.

[gringer]

[FWIW, if it's in a single line, then it's not a fastq formatted file]

I can't see any '--12' option in the help output of bowtie (could you point to the bowtie manual where it talks about this option?), but do notice that both bowtie and bowtie 2 support the 'raw' single-line file input type, and bowtie2 also accepts Illumina's qseq format:

Bowtie(v1):
Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  -f                 query input files are (multi-)FASTA .fa/.mfa
[b]  -r                 query input files are raw one-sequence-per-line[/b]
Bowtie2:
 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
[b]  --qseq             query input files are in Illumina's qseq format[/b]
  -f                 query input files are (multi-)FASTA .fa/.mfa
[b]  -r                 query input files are raw one-sequence-per-line[/b]

The raw format mentioned in that help doesn't seem to be what you want. The bowtie manual states "one sequence per line, without quality values or names. All quality values are assumed to be 40 on the Phred quality scale." No tabs to be found.

[Tonnny97]

Thanks gringer!

Sorry for my unclear description.
--12 is not an option. As mentioned in the Bowtie1 manual:

http://bowtie-bio.sourceforge.net/manual.shtml#command-line

It is one of the choices for read file input.

Usage:
bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]

<r>
Comma-separated list of files containing a mix of unpaired and paired-end reads in Tab-delimited format. Tab-delimited format is a 1-read-per-line format where unpaired reads consist of a read name, sequence and quality string each separated by tabs. A paired-end read consists of a read name, sequnce of the #1 mate, quality values of the #1 mate, sequence of the #2 mate, and quality values of the #2 mate separated by tabs.

[gringer]

Huh, not sure how I missed that. I'm guessing based on a search through the bowtie2 manual for the word 'tab' that this option doesn't exist in bowtie2.

FWIW, you should be able to convert a single-end tab-separated file to fastq with a quick awk script:

$ cat test.seq 
Read1   ACATCAGGT       AFFABABAA
Read2   ATTACAGAA       DEADBEEFA
$ awk -F '\t' '{print "@" $1 "\n" $2 "\n+\n" $3}' test.seq
@Read1
ACATCAGGT
+
AFFABABAA
@Read2
ATTACAGAA
+
DEADBEEFA
$ awk -F '\t' '{print "@" $1 "\n" $2 "\n+\n" $3}' test.seq > test.fastq

Mixed reads would be a bit more complicated, and probably better output to separate files, so I'd degenerate to writing a Perl (or Python) script to do that because I'm not so comfortable with awk.

[Tonnny97]

Thanks for gringer's information and advices.