<![CDATA[BOL: All site questions]]> https://bioinformaticsonline.com/answers/?offset=120 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 https://bioinformaticsonline.com/answers/view/26599/is-there-any-database-other-than-geo-ncbi-ncbi-src-database-to-get-exome-data Thu, 10 Mar 2016 13:28:46 -0600 https://bioinformaticsonline.com/answers/view/26599/is-there-any-database-other-than-geo-ncbi-ncbi-src-database-to-get-exome-data <![CDATA[Is there any database other than GEO ncbi, ncbi src database to get exome data??]]> Iam searching for the exome data for an eye disease "Glaucoma" obtained by next generation sequencing platform but unfortunately  i am not able to get that data. I have already searched ncbi SRC, GEO data sets of ncbi but no data is available. Is there any database other than these to get data in FASTQC format?? Or any article related to glaucoma where information about datasets is available.

thanks

]]> Nadia Baig https://bioinformaticsonline.com/answers/view/26579/comparison-of-mapping-tools Tue, 08 Mar 2016 07:34:19 -0600 https://bioinformaticsonline.com/answers/view/26579/comparison-of-mapping-tools <![CDATA[Comparison of mapping tools !]]> There are many mapping tools, and each one has its own specifications. Once we have two or more tools for similar purposes, how can we say which tool is better?

]]> pradyumna Jayaram https://bioinformaticsonline.com/answers/view/26563/whar-are-n50-and-l50-of-a-contig-assembly-file-how-to-calculate-it Fri, 04 Mar 2016 05:46:52 -0600 https://bioinformaticsonline.com/answers/view/26563/whar-are-n50-and-l50-of-a-contig-assembly-file-how-to-calculate-it <![CDATA[Whar are N50 and L50 of a contig assembly file? How to calculate it?]]> I am currently dealing with new contig assembly dataset, and bit confused about N50 and L50 stuff ....

]]> Gudiya Pal https://bioinformaticsonline.com/answers/view/26549/what-is-a-oligodomain Tue, 01 Mar 2016 00:27:06 -0600 https://bioinformaticsonline.com/answers/view/26549/what-is-a-oligodomain <![CDATA[what is a oligodomain ?]]> Amala Arumugam https://bioinformaticsonline.com/answers/view/26460/fasta-error-with-sift Thu, 25 Feb 2016 01:01:34 -0600 https://bioinformaticsonline.com/answers/view/26460/fasta-error-with-sift <![CDATA[FASTA error with Sift ?]]> Can anyone tell me how to rectify the problem in Sift ? While am running the fasta sequence of my protein of interest its showing error after few minutes and  few times it giving job id but am not getting the result

]]> Amala Arumugam https://bioinformaticsonline.com/answers/view/26289/does-any-one-knows-bioconducter Fri, 05 Feb 2016 06:00:19 -0600 https://bioinformaticsonline.com/answers/view/26289/does-any-one-knows-bioconducter <![CDATA[Does any one knows Bioconducter]]> kritika mishra https://bioinformaticsonline.com/answers/view/26162/bioinformatics-study-partner Sat, 23 Jan 2016 11:46:01 -0600 https://bioinformaticsonline.com/answers/view/26162/bioinformatics-study-partner <![CDATA[bioinformatics study partner]]> where can i find a bioinformatics study partner online , to discuss , work toghether in the field 

]]> karimse07 https://bioinformaticsonline.com/answers/view/25975/protein-structure-and-domain-help-needed Mon, 11 Jan 2016 00:43:47 -0600 https://bioinformaticsonline.com/answers/view/25975/protein-structure-and-domain-help-needed <![CDATA[Protein structure and domain help needed !]]> what does it mean in protein structure as one domain, two domain, three domain and so on ? can anybody help me to know about this ? if there is any link or related article plz do a share.

PS: in relation protein structure

]]> Amala Arumugam https://bioinformaticsonline.com/answers/view/25829/german-universities-providing-masters-in-bioinformatics Sun, 03 Jan 2016 01:38:16 -0600 https://bioinformaticsonline.com/answers/view/25829/german-universities-providing-masters-in-bioinformatics <![CDATA[German universities providing Masters' in Bioinformatics?]]> Hello fellow bioinformaticians,

Does anyone know of any German universities providing Masters' in Bioinformatics in English language?(besides FU Berlin)

Thank you in advance!

]]> Manas Joshi