<![CDATA[BOL: how to determine @RG tags from a FastQ header??]]> https://bioinformaticsonline.com/answers/view/26714/how-to-determine-rg-tags-from-a-fastq-header? https://bioinformaticsonline.com/answers/view/26714/how-to-determine-rg-tags-from-a-fastq-header Sat, 19 Mar 2016 04:04:03 -0500 https://bioinformaticsonline.com/answers/view/26714/how-to-determine-rg-tags-from-a-fastq-header <![CDATA[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 <==
@HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
TNACTGTTTCTCTAAAACCTTACAAGAAAAACTAAGCTTCTCTAAACTTGTATTCATTATGGGAGNATGNCA
+HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
C)CCCGGGGGIIIIIIIIIIIIIHIIIIIIIIIIIGIHIIIIIHHIIIHIHIIHIIHIIHAAA?B#######
@HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
ANGTTGTCTAAAGTAATAACTCCATTGGCTATTATTTTCTAAACATCTAAAACAAAACTTAACTANCGANAT
+HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
B(B?BGGGGGIIIICIIIIIIIIIIIIIIIIHIHIIIIIIIIIIIIGIIIIIIFIIIIGIEEECE#######
@HWUSI-EAS754_0001:4:1:6654:1035#GCCAAT
TNTTTAAATAAAAGGTTCTGTATCTTGATCCTGAAGTATCCTGTAATAGCCTACAGTGAAAAGAANACANTT

==> ERR042057_2.fastq <==
@HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
AAGAAATTTATTCCTGCAGATCAATATTTCCCGCAACCACTTGAGAATTTCTGTGCTACTAAGCATTTGATG
+HWUSI-EAS754_0001:4:1:5605:1034#GCCAAT
IIHHHIIIIHIHIIHGIIIIIIGIHGGG4D<??:@CC?C@CGEDFGEEEEGH>EH<BEEFED8CFBEBEB?#
@HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
AGAAACTGAGCTGAAGAGGGTAAAAGTCCTTGGCTCAGGTGCTTTTGGAACGGTTTATAAAGTAAGTAAAAA
+HWUSI-EAS754_0001:4:1:6122:1035#GCCAAT
HHGHHHHHHHHHHHHHFHHHHHHFFHEHHHGHGH<DBDB=DDDDDBFCDEB><BB>CBDB=D?BE?8A?A37
@HWUSI-EAS754_0001:4:1:6654:1035#GCCAAT
CTAAACCCCCCCCCACCCCACCCCCCCACCACACCAACCCCACCCACACACCCCAACCACCCTCACACTCTC



Tail:

==> ERR042057_1.fastq <==
+HWUSI-EAS754_0001:4:120:19005:21176#GCCAAT
G>D>DBDDGBGGE@>EGGGGBG;GGGGDBG##########################################
@HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
GAGAAAGAATTCAAACTGATTTTTCTTTTCTTNNNNNNNNNNNNGGGCACTNNNNNNNNNNNTGGCCCTCCT
+HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
IIIEIIIHIIIHIIIIIIEIHIIIIHHIII##########################################
@HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
CGGGGAAGAGCGCCAGCACCGAGGTGCCAGGTNNNNNNNNNNNNGCGGAGAANNNNNNNNNNATCATGCAGT
+HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
HIGIIHIIIIIIIHDIIHIIGGII@DD?BD##########################################

==> ERR042057_2.fastq <==
+HWUSI-EAS754_0001:4:120:19005:21176#GCCAAT
?AA6A?A?A?A@@<A#########################################################
@HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
ATTAGCAGACATATATCTTTTCTCTGAAATCTAAATACTTGCAGAAATACTAATTTTCATTTTATATTATGT
+HWUSI-EAS754_0001:4:120:19024:21176#GCCAAT
HGHHFFEHEHHHFHHBDBH:DGGGEHFBHHHDGHHHDHDHBGGGEGGEGGGBGGG(+:;;F<=F@;FE?EGG
@HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
CAAAGCAGGCCCCACGAGGCTGGCTGCGTGCGGGGTGCTCACCCGTGGCCGGTCCTGCGGGGCCCGCTGATC
+HWUSI-EAS754_0001:4:120:19130:21175#GCCAAT
HFHHHHHHEHHHHHHA3E8GD>GGBBEEBEGG<G>?AD>GGGEEGD>G@DGD3D##################

 

 

 

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

 

]]> Nadia Baig