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Old 05-04-2018, 12:26 PM   #3
cursecatcher
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Location: Italy

Join Date: May 2018
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Quote:
Originally Posted by Richard Finney View Post
Check your chromosome names.
Are they "chr" style in both bed and bam?
Hi Richard, thanks for the reply.
About your question, I think not.

In the bed file I have record like this:
Code:
chr1    11123000        11123242        chr1:11123018-11123218
chr1    16696418        16696674        chr1:16696447-16696647
while in the SAM file (and consequently in the BAM file) I have record like that:

Code:
M03971:33:000000000-BN5NL:1:2114:12003:16132    99      NC_000016.9     24163387        255     151M    =       24163431        194     TGATCGGTGGTGA
TGGGTTAGGTAGAGTGTATTAGTTCGTTTTTATGTTGTTGATAAAGATATATTCGAGATTGTGTAATTTATGAAAAAGAGGTTTAATGGATTTGGGGAGGTTTTAATTATGGTGGAAGGTTAAAGTTATGTTTTATAT BCCCCCCBBC
ABGGGGGGFGGGGHHHHFGGHHHHHHHHGGHGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHFHHHHGGHHHHHHHHHHHHHHHHGGFGGEHHGHHHHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHH NM:i:1
  ZS:Z:++
Ps. the SAM file is the result of an alignment with BSMAP.

Is this the problem? How can I resolve it?
Nicola
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