I get an error while uploading BAM file. I used bowtie to map small-RNA reads against one mRNA fasta file. I sorted and indexed the bam file but I get the error in uploading it on IGV:
Error loading BAM file: htsjdk.samtools.SAMException: Sequence name 'X64322.2:1-409,510-527,628-676,777-1929' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'
Could someone help me please?
This is my fast file (ref) head: ```
X64322.2:1-409,510-527,628-676,777-1929 Chironomus tentans partial BR1 gene for balbiani ring protein 1 precursor AGTTTTGGGAATTCATTTCCAGACTTCTCCCAAGTAAAATAAAAGAAGTGTGAAGTAAGTGAAAACAAAC ```
and here is my BAM file header:
samtools view file.bam | head
NB501365:508:HJF2HBGXF:2:13202:14744:16156 16 X64322.2:1-409,510-527,628-676,777-1929 16 255 61M * 0 0 TTTCCAGACTTCTCCCAAGTAAAATAAAAGAAGTGTGAAGTAAGTGAAAAAAAACCAAGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:1 MD:Z:50C10 NM:i:1 XM:i:2
NB501365:508:HJF2HBGXF:3:13401:10152:8366 16 X64322.2:1-409,510-527,628-676,777-1929 16 255 61M * 0 0 TTTCCAGACTTCTCCCAAGTAAAATAAAAGAAGTGTGAAGTAAGTGAAAAAAAACCAAGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
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Apex92 •
1 answer
A reference chromosome cannot be named "X64322.2:1-409,510-527,628-676,777-1929" . see the SAM Spec: https://samtools.github.io/hts-specs/SAMv1.pdf
Reference sequence names may contain any printable ASCII characters in the range[!-~]apart frombackslashes, commas, quotation marks, and brackets—i.e., apart from ‘\ , "‘’ () [] {} <>’—and may notstart with ‘*’ or ‘=’
why ? because you could not query a specific a region 100-200 of such file:
eg. samtools view your.bam X64322.2:1-409,510-527,628-676,777-1929:100-200
you should rename your reference.
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