SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Best source for GTF file for use with TopHat/Cufflinks sdarko Bioinformatics 17 12-14-2012 11:48 AM
tophat junctions.bed file upendra_35 RNA Sequencing 2 10-23-2012 07:17 AM
How to make sense of Tophat's output file 'junctions.bed' gsinghal RNA Sequencing 4 09-03-2012 06:49 AM
Missing Junctions in Tophat! ( after providing a known junctions & gene models files) avi Bioinformatics 2 08-02-2011 04:21 PM
whether tophat can find interchromosomal hits when junctions are provided... nturay Bioinformatics 0 02-09-2011 05:12 PM

Reply
 
Thread Tools
Old 10-25-2012, 03:35 PM   #1
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default TopHat did not find any junctions in GTF file

I can not figure out why I am getting the message, 'TopHat did not find any junctions in GTF file',
as well as the error, 'Couldn't build bowtie index with err = 1'.

When this file, TAIR10_GFF3_genes.gff, is used, eveything works fine.
HTML Code:
Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
Chr1	TAIR10	gene	3631	5899	.	+	.	ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
Chr1	TAIR10	protein	3760	5630	.	+	.	ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
However, when this file, ath_miRBase_miRNA_Cap-Chr_V.gff3, is used, the error appears.
HTML Code:
Chr1	TAIR10	chromosome	1	30427671	.	.	.	ID=Chr1;Name=Chr1
Chr1	TAIR10	miRNA_primary_transcript	28500	28706	.	+	.	ID=MI0005394_1;accession_number=MI0005394;Name=ath-MIR838
Chr1	TAIR10	miRNA	28635	28655	.	+	.	ID=MIMAT0004260_1;accession_number=MIMAT0004260;Name=ath-miR838;derives_from=MI0005394_1
Chr1	TAIR10	miRNA_primary_transcript	78927	79037	.	-	.	ID=MI0000199_1;accession_number=MI0000199;Name=ath-MIR165a
The command line is (the only difference being the file after the -G switch).

./tophat --library-type fr-unstranded
-o /A_ATCACG_set1_mRNA_TH-out
-G /ath_miRBase_miRNA_Cap-Chr_V.gff
/TAIR10_C_Bt2
/A_ATCACG_L008_R1.fastq

I have used bowtie2-inspect -n, and made sure the names are the same in the genome index, TAIR10_C_Bt2, and the gff3 file.
The formatting of the two gff files (the one that does work and the one that doesn't) seems exactly the same to me.
mattanswers is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO