Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
SpliceMap: all reads less than 50bp after clipping belgravia Bioinformatics 1 12-12-2016 02:04 PM
SpliceMap gene annotation files paulorapazote RNA Sequencing 0 06-14-2012 01:48 AM
SpliceMap 3.3 Released - Improved long-read sensitivity john_mu Bioinformatics 19 08-08-2011 03:39 PM
SpliceMap Gene annotations file for hg19 trickytank Bioinformatics 0 01-18-2011 04:44 PM
SpliceMap 3.2.1: Announcing addition of Bowtie support john_mu Bioinformatics 6 06-05-2010 07:44 PM

Thread Tools
Old 08-10-2017, 07:27 AM   #1
Junior Member
Location: coimbatore

Join Date: Dec 2014
Posts: 3
Post SpliceMap


I am trying SpliceMap for finding splicing in my reads. I have fastq formats (pair end- 2 files). I have reference genome in fasta format and gene annotation file as well. I have built bowtie index for my genome. But when i run SpliceMap, I am getting the following error

ERROR: The following chromosome does not exist in the bowtie index
1 | /home/ | pos:71 - 30812903
Please make sure that all chromosomes are contained within the bowtie index

I could not rectified this error. I tried so many times to rebuild bowtie index files using bowtie software and again i am getting these errors. Can anyone help me ?
shensteff is offline   Reply With Quote

bowtie 2 indexes, splicemap

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 10:09 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO