Nadia Baig
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Question: Question: how to determine @RG tags from a FastQ header??
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Nadia Baig |
Question: how to determine @RG tags from a FastQ header??
i have downloaded sra file and converted into paired end FastQ having following headers: @HWUSI-EAS754_0001:4:1:5605:1034#GCCAT The head and tail of file are as follow Head: ==> ERR042057_1.fastq <==
How to determine the @RG ?
I'm using the following command to add @RG tag: java -jar picard.jar AddOrReplaceReadGroups I=input.bam O=output.bam RGID=? RGLB=? RGPL=illumina RGPU=? RGSM=?
What should be the @RG tags values for following parameters: RGID=? RGLB=? RGPL=illumina RGPU=? RGSM=? The link for SRA data is : http://www.ncbi.nlm.nih.gov/sra/ERX019190[accn
Thankyou in advance
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To see the read group information for a BAM file, use the following command.
samtools view -H sample.bam | grep '@RG'
Option Description of AddOrReplaceReadGroups
INPUT (String) Input file (BAM or SAM or a GA4GH url). Required.
OUTPUT (File) Output file (BAM or SAM). Required.
SORT_ORDER (SortOrder) Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate}
RGID (String) Read Group ID Default value: 1. This option can be set to 'null' to clear the default value.
RGLB (String) Read Group library Required.
RGPL (String) Read Group platform (e.g. illumina, solid) Required.
RGPU (String) Read Group platform unit (eg. run barcode) Required.
RGSM (String) Read Group sample name Required.
RGCN (String) Read Group sequencing center name Default value: null.
RGDS (String) Read Group description Default value: null.
RGDT (Iso8601Date) Read Group run date Default value: null.
RGPI (Integer) Read Group predicted insert size Default value: null.
RGPG (String) Read Group program group Default value: null.
RGPM (String) Read Group platform model Default value: null.