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IGV error: Error loading SAM header: For sequence 34711, text and binary have different lengths in file.

HI,

I have sam file and I converted into a bam and later sorted it. I also created bam index for the sorted_bam file. When I am trying to load the bam files into IGV, I am getting the following error:

Error loading SAM header: For sequence 34711, text and binary have different lengths in file.

Can I anyone guide me why the error is popping out.

Thanks in advance

rna-seq bam igv
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updated by dyollluap dyollluap • written by EVR EVR

I have sam file and I converted into a bam and later sorted it. I also created bam index for the sorted_bam file.

Please be as complete as possible and add the following:

  • the commands you used for sam -> bam, sorting and indexing
  • Your version of samtools and igv
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written by WouterDeCoster WouterDeCoster 
My samtools version : 1.3
My IGV version: 2.3.97

Command for converting sam to bam file:

samtools view --threads 40 -F 4 -bS -o mySample.bam -O bam mySample.sam

Command for sorting:

samtools sort --threads 40 -o Sorted_mySamlpe.bam -O bam mySample.bam

Command for indexing:

samtools index mySample.bam

• 0 views • link
written by EVR EVR

All i did was mapping the reads onto transcriptome and obtained a sam file which is later converted into bam as I shown below. Is there any way to look which transcript_Id/Contig_Id got corrupted? or should I have to remap

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written by EVR EVR

1 answer

Usually I see that different lengths in file error when different versions of the reference assembly have been used in whatever process is being performed. In this case, if the reference.fa you used for building a bam index is different from the original sam alignment, you get this error.

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written by dyollluap dyollluap

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