Eland export to sam

[bair]

Hello all,

After converting Eland alignment export files to sam, I tried to convert sam to bam by samtools view -bt ref.fa.fai,

what do these mean shown on the screen? Thanks.

[sam_read1] reference 'chr11.fa' is recognized as '*'.
[sam_read1] reference 'chr6.fa' is recognized as '*'.
[sam_read1] reference 'chr6.fa' is recognized as '*'.
[sam_read1] reference 'chr11.fa' is recognized as '*'.
[sam_read1] reference 'chr11.fa' is recognized as '*'.
[sam_read1] reference 'chrY.fa' is recognized as '*'.
[sam_read1] reference 'chr1.fa' is recognized as '*'.
[sam_read1] reference 'chr1.fa' is recognized as '*'.
[sam_read1] reference 'chrX.fa' is recognized as '*'.

[pharmbot]

@bair,
Did you find a solution for this problem?

[pharmbot]

Nevermind... The ELAND alignment from our Core used a 'chrN.fa' reference, whereas the hg19.fa uses just 'chrN'. Adding a --nofa tag to export2sam.pl with "if($nofa > 0){$t[EXPORT_CHROM] =~ s/.fa//g};" got us back on track.

[hrajasim]

Nevermind... The ELAND alignment from our Core used a 'chrN.fa' reference, whereas the hg19.fa uses just 'chrN'. Adding a --nofa tag to export2sam.pl with "if($nofa > 0){$t[EXPORT_CHROM] =~ s/.fa//g};" got us back on track.

OR, you could just do a sed s/.fa// on the input file before doing export2sam.pl

[kreitinger]

How did you convert the ELAND alignment ouput file to sam? I have scoured the web/literature and cannot find out how to do this.

[hrajasim]

How did you convert the ELAND alignment ouput file to sam? I have scoured the web/literature and cannot find out how to do this.

One way to do this is using Illumina's casava software's helper script illumina2sam.pl

[kreitinger]

Thanks, I will look into that. One problem, though, is I do not have access to the Illumina software and was hoping there was some opensource software instead.

[jeny]

there is a script export2sam.pl in samtools package (opensource) that may help you.