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Old 04-14-2010, 09:45 AM   #1
bair
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Default 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 '*'.
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Old 04-01-2011, 08:30 AM   #2
pharmbot
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@bair,
Did you find a solution for this problem?
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Old 04-02-2011, 01:25 PM   #3
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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.
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Old 05-12-2011, 08:56 AM   #4
hrajasim
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Quote:
Originally Posted by pharmbot View Post
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
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Old 06-28-2011, 01:14 PM   #5
kreitinger
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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.
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Old 06-28-2011, 01:28 PM   #6
hrajasim
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Quote:
Originally Posted by kreitinger View Post
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
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Old 06-28-2011, 01:43 PM   #7
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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.
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Old 06-30-2011, 08:15 AM   #8
jeny
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there is a script export2sam.pl in samtools package (opensource) that may help you.
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