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Old 04-01-2012, 05:28 AM   #1
ramirob
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Location: Vermont

Join Date: Apr 2012
Posts: 14
Default [sam_read1] reference 'chrN.fa' is recognized as '*'

Hello,

I aligned some human samples with Casava, and then converted the alignments to SAM using samtools:

llumina_export2sam.pl --read1=file_R1.export.txt.gz --read2=file_R2.export.txt.gz > file.sam

Then I try to convert to bam:

samtools view -bt genome.fa.fai file.sam > file.bam

but I get a lot of

[sam_read1] reference 'chr8.fa' is recognized as '*'.
[sam_read1] reference 'chr11.fa' is recognized as '*'.
etc.

There was a similar thread that suggested changing the header as follows:

The first line needs to be header.
The second line needs to be a dummy read group line
The next lines need to contain the chromosomes and their lengths.

An example of a good header is as follows:

@HD VN:1.0 SO:unsorted
@RG ID:unknownReadGroup SM:unknownSample
@SQ SN:chrI AS:ce6_32r_index LN:15072421
@SQ SN:chrII AS:ce6_32r_index LN:15279323
@SQ SN:chrIII AS:ce6_32r_index LN:13783681
@SQ SN:chrIV AS:ce6_32r_index LN:17493785
@SQ SN:chrM AS:ce6_32r_index LN:13794
@SQ SN:chrV AS:ce6_32r_index LN:20919568
@SQ SN:chrX AS:ce6_32r_index LN:1771885


where do I get all of that information? I also might have to do this over and over again so I was looking for some software or precise ways so that I can write a script to do it.

Thanks in advance,

Ramiro
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Old 03-25-2013, 03:39 AM   #2
naman.neoanderson007
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Location: ahmedabad,India

Join Date: Mar 2013
Posts: 1
Default

Hi, Ramiro

I have just entered in 'seqanswers' and saw your question

I suggest you to check your GENOME file - "genome.fa.fai"
Is it in proper FASTA format ?

Correct FASTA formated GENOME file will solve your problem.

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