Error in sam to bam conversion after bowtie alignment

Question

[Maguelonne]

I used this command line in bowtie:

bowtie -v 0 -m 1 ref file1.fastq file2.sam

and now I'm trying to convert the sam file I obtained:

samtools view -b -S file2.sam > file2.bam

and I get this error (even if I specify the -t ref.fa.fai option):

[W::sam_read1] parse error at line 1
[main_samview] truncated file.

Here's the header of my sam file:

HWI-1KL110:149:HAUWDADXX:1:1101:1419:2097 1:N:0:ATCACG  -       MT      7644    TATCACCTTTCATGATCACGCC  IEIFFIIIIIEEDDDDD8DDD?  0
HWI-1KL110:149:HAUWDADXX:1:1101:2046:2200 1:N:0:ATCACG  +       17      57918633        TAGCTTATCAGACTGATGTTGACT        CCCFFFFFHHDFHIIIIJJIJJJI        0
HWI-1KL110:149:HAUWDADXX:1:1101:3118:2245 1:N:0:ATCACG  +       17      28444112        TGAGGGGCAGAGAGCGAGACTTT @@?DDD1D8CCDFE<FG6??CDE 0

Can someone help me?

[Thibault D.]

Hi. Have you tried the following command ? :

samtools view -bhS file2.sam > file2.bam

(with -h option)

[Maguelonne]

Yes, it doesn't work either.

Answer 1

[thackl]

Your output is not SAM. I think it's bowtie legacy output (another tsv format). You need to use bowtie --sam

[Maguelonne]

You're right! Thanks!

[Johan Zicola]

There are 2 possibilities in Bowtie to get an output in SAM format:

• Add the tag -S <output.sam> if one wants directly the SAM file (space consuming)
• In case one wants to pipe the sam output directly in samtools to get a sorted bam file (smaller), add flag --sam such as bowtie --sam | samtools view -bS - > <output.sorted.bam>

NB: Most parameters are omitted in the bowtie command.