How to separate Miseq data and Hiseq data

Question

[Bioinfo]

Hello everyone please i have question i have a file containing Mi seq data and Hi seq data Hi seq reads starts with @HI and Mi seq reads starts with MI. like this for exemple

@HI name
ACATATATATAT
+
HJKSKSKSKSK
@MI name
TCTAGATAGGCTATCAGATGAT
+
HYUHJKKKKKJJJKKKKKKHHYH

my question is how i can separate my seq reads and Hi seq reads .

Thank you

Answer 1

[JC]

You can use grep command:

grep -A3 "@MI" FILE > miseq_reads.fastq
grep -A3 "@HI" FILE > hiseq_reads.fastq

Answer 2

[cschu181]

grep -A3 "^@HI" fastq_file | grep -v "\-\-" > hiseq_reads_file
grep -A3 "^@MI" fastq_file | grep -v "\-\-" > miseq_reads_file

[Bioinfo]

Thank you very much

[ATpoint]

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