Eland export to sam

bair · 04-14-2010, 09:45 AM

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 · 04-01-2011, 08:30 AM

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

pharmbot · 04-02-2011, 01:25 PM

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 · 05-12-2011, 08:56 AM

Quote:

Originally Posted by 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.

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

kreitinger · 06-28-2011, 01:14 PM

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 · 06-28-2011, 01:28 PM

Quote:

Originally Posted by 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.

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

kreitinger · 06-28-2011, 01:43 PM

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 · 06-30-2011, 08:15 AM

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

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04-14-2010, 09:45 AM	#1
bair Member Location: London Join Date: Jan 2010 Posts: 65	Eland export to sam 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 '*'.

04-01-2011, 08:30 AM	#2
pharmbot Junior Member Location: Connecticut Join Date: Mar 2011 Posts: 2	@bair, Did you find a solution for this problem?

04-02-2011, 01:25 PM	#3
pharmbot Junior Member Location: Connecticut Join Date: Mar 2011 Posts: 2	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.

06-28-2011, 01:14 PM	#5
kreitinger Member Location: Madison, WI Join Date: May 2011 Posts: 10	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.

06-28-2011, 01:43 PM	#7
kreitinger Member Location: Madison, WI Join Date: May 2011 Posts: 10	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.

06-30-2011, 08:15 AM	#8
jeny Member Location: france Join Date: Mar 2010 Posts: 16	there is a script export2sam.pl in samtools package (opensource) that may help you.