Hi Guys,
I hope it does not turn as a stupid question but this issue is driving me crazy. I have a reference genome A that contains chromosome I am not interested in. I used a python software to generate a new reference genome B with only some of the chromosomes of A. A and B have, as a way of example, Chr1 in common.
If I align all my reads on the complete reference genome A I get for Chr1 an average coverage of 10
If I align all my reads on chromosome B I get for Chr1 an average coverage of 2.
This does not make any sense! Moreover in the second case I obtain sam files that are smaller than the original reads fastq file, which I guess is also impossibile.
Any idea of such a strange result
I appreciate your help
I hope it does not turn as a stupid question but this issue is driving me crazy. I have a reference genome A that contains chromosome I am not interested in. I used a python software to generate a new reference genome B with only some of the chromosomes of A. A and B have, as a way of example, Chr1 in common.
If I align all my reads on the complete reference genome A I get for Chr1 an average coverage of 10
If I align all my reads on chromosome B I get for Chr1 an average coverage of 2.
This does not make any sense! Moreover in the second case I obtain sam files that are smaller than the original reads fastq file, which I guess is also impossibile.
Any idea of such a strange result
I appreciate your help
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