The best output format for paired-end alignment using bowtie

[chedonat]

Hi all,
I successfully used bowtie to perform some single end alignments.
Now, I would like to perform some paired-end alignments using bowtie 2, and I am just wondering if I am oblige to use the SAM output format option.
How will be the output if I don't specified this option?
The manual only clearly mention the SAM output format.
What is the best of the two possibilities.
Many thanks

[gringer]

I think bowtie2 only outputs in SAM format. If you would prefer a sorted BAM (because of smaller file size and better searching), you can pipe through samtools:

bowtie2 -t -p 30 bowtie2_database -U reads_SE.fastq \
| awk '{if($12 != "XM:i:0"){print $0}}' | samtools view -S -b - | samtools sort -m 10000000000 - reads_SE_vs_database_bowtie2_default

[I also exclude unmapped reads from the BAM output with AWK because I'm not interested in them]

[jbrwn]

I think bowtie2 only outputs in SAM format. If you would prefer a sorted BAM (because of smaller file size and better searching), you can pipe through samtools:

bowtie2 -t -p 30 bowtie2_database -U reads_SE.fastq \
| awk '{if($12 != "XM:i:0"){print $0}}' | samtools view -S -b - | samtools sort -m 10000000000 - reads_SE_vs_database_bowtie2_default

[I also exclude unmapped reads from the BAM output with AWK because I'm not interested in them]

can't you skip the awk pipe by adjusting your samtools view with:
samtools view -SbF 4 -

[swbarnes2]

I think by default, bowtie won't return unampped reads anyway. But I think using samtools to filter is way easier than piping through awk. It's also a little faster if you add the -u to the samtools view command. It will make an uncompressed .bam. But since you are going to sort anyway, that'll get you to the sorted file a little faster, and once you have the sorted file, you won't need the unsorted one. sort will complain that the .bam doesn't look like it has the right EOF character, but it still works.

[gringer]

can't you skip the awk pipe by adjusting your samtools view with:
samtools view -SbF 4 -

I guess so, I hadn't noticed those filter options of samtools view. Thanks.