Changes between Version 56 and Version 57 of SOPs/qc_shortReads

Timestamp:

12/15/20 10:49:10 (4 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -311 +311 @@
 The *common.out reads should be used for paired-read mapping.
 
+== Select a subset of reads by read ID  ==
+
+To get a list of read IDs from a fastq file, one can use a command like
+{{{
+zmore Reads.fq.gz | awk 'NR % 4 == 1' | perl -pe 's/^\@//' >| Selected_read_IDs.txt
+}}}
+
+Using this list of read IDs, one can extract this subset of reads from a larger fastq file (using [[https://github.com/lh3/seqtk|seqtk]]) like 
+{{{
+seqtk subseq All_reads.fq.gz Selected_read_IDs.txt >| Selected_reads.fq
+}}}
+
 \\
 = Analyzing potential species composition/contamination of reads in a fastq file =