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Old 03-27-2015, 07:33 AM   #1
Location: china,guangzhou

Join Date: Mar 2015
Posts: 17
Default how can I retrieve one read sequence?

Hi, I use Integrative genomic Viewer to find one Read which mate is mapped=no.
This no mapped pair-end read may be a result from structural variation. So, if I know one read ID and its one end sequence, How can I get its pair-end sequence from raw Data.

hujiacun is offline   Reply With Quote
Old 03-27-2015, 08:00 AM   #2
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Location: East Coast USA

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If your sequence files are not compressed:

$ cat file.fastq | grep -A 3 "read_ID_you_want"
If they are compressed:

$ zcat file.fastq.gz | grep -A 3 "read_ID_you_want"
If you only want sequence (not full fastq record) then replace 3 with 1.
GenoMax is offline   Reply With Quote

mate pair rescue, pair end reads

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