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Recent Replies
Answer: How to not align reverse complementary reads?
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Basically the same as @liorglic says, remove the RCs prior to building the index. The convention for fasta files for genomic references (as…
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liorglic
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This question is too general. Give more details on your input and desired output. Also, what have you tried so far?
Answer: How to not align reverse complementary reads?
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I don't think this is possible with BWA. Why don't you just remove the antisense sequence from your fasta? You can then map to the sense se…
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Any chance one of your input fasta files contains multiple records with the same name? In any case, the best place to ask about Maker is [t…
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Personally I prefer to avoid SRA altogether, as I find it to be hard to use and slow. Instead I use [ENA][1], which mirrors all the SRA dat…
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Just to clarify (as per the OP's question): R2 **is not** the reverse complement of R1. R1 and R2 come from different places in the genome,…
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Key thing to keep in mind is you are sampling/sequencing a fragment of DNA (from a library of such fragments made from a sample) from both …
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it looks like the names of the chromosome are in the bin filename. Here is my directory for human:
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Thanks for your suggestions. You may have misunderstood my question. I need output.bam to contain all regions in big.bam, not just small.be…
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