I mapped read to reference but any suggestions how to extend them?
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madhu.9124 •
Extension of reads
Hi,
I want to extend the read to the 3' or 5' end of the read. Kindly suggest some command.
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boczniak767
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madhu.9124 •
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madhu.9124 •
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Well, a single read can't be extended.
- If you have a reference sequence: mapping reads to the reference and extend them.
- If reference is not available: assembling de novo, and extending reads.
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shenwei356
retrieving mapping location and extending from reference by scripts or tools.
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shenwei356
I have the same question. It is trivial to extend bed intervals, but what about extending mapped reads in bam file? I think samtools can't do that.
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boczniak767
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Awk, and more elaborate: bedtools slop. In R: GenomicRanges package with the resize option.
Please elaborate more on which data you have and what you aim to obtain. Your question doesn't contain sufficient information.