How to extract sequence lines from FASTQ file?
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I have FASTQ formatted Illumina sequence file like this:
@ERR009148.2485 IL26_1382:7:1:224:616 length=36
ATCACATGCTCCTTGTTCTGCAGCTTGGTGCGGATG
+ERR009148.2485 IL26_1382:7:1:224:616 length=36
>>>>>>>>>>>>>>>>>>>>>>5>>->>*
@ERR009148.2486 IL26_1382:7:1:914:59 length=36
AAAGAAGTAAAATAAGAAGGCAATGCTTGTGGAAGG
+ERR009148.2486 IL26_1382:7:1:914:59 length=36
.>>74::1>174151/7152313,3&003,00&2%2
@ERR009148.2487 IL26_1382:7:1:251:589 length=36
GCCATAAACACCCCAGCACCACATTCATCAGAAGGG
+ERR009148.2487 IL26_1382:7:1:251:589 length=36
>>>>>>>>>>>>>>>>>>>>>>8>>>>>>>>7
@ERR009148.2488 IL26_1382:7:1:911:194 length=36
ATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAG
+ERR009148.2488 IL26_1382:7:1:911:194 length=36
>>=>>>>>>>=;>7>==<<7;=67=/57/57
I need to extract only the raw sequences from each record. What
sed
command can be used for that?
Expected output:
ATCACATGCTCCTTGTTCTGCAGCTTGGTGCGGATG
AAAGAAGTAAAATAAGAAGGCAATGCTTGTGGAAGG
GCCATAAACACCCCAGCACCACATTCATCAGAAGGG
ATTGAGGTGGAGTAGATTAGGCGTAGGTAGAAGTAG
Asked by iiii
(11 rep)
Oct 13, 2017, 05:40 AM
Last activity: Feb 21, 2024, 04:17 AM
Last activity: Feb 21, 2024, 04:17 AM