Changes between Version 63 and Version 64 of SOPs/qc_shortReads


Ignore:
Timestamp:
08/19/24 12:43:07 (5 months ago)
Author:
ibarrasa
Comment:

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  • SOPs/qc_shortReads

    v63 v64  
    306306
    307307During quality control, if low-quality reads have been removed for any reason, some reads may not have a paired end at the other end.  This can cause problems with mapping programs.
    308 
     308* '''Method 1''':
    309309Sample command:
    310310
    … …  
    318318
    319319The *common.out reads should be used for paired-read mapping.
     320
     321* '''Method 2''':
     322For fastq.gz files use the seqkit instead
     323[https://bioinf.shenwei.me/seqkit/usage/ seqkit]
     324{{{
     325seqkit pair -1 sequence.1_1.filt.fq.gz  -2  sequence.1_2.fil.fq.gz   # fastq inputs
     326}}}
     327
    320328
    321329== Select a subset of reads by read ID  ==