Go Back   SEQanswers > Applications Forums > Genomic Resequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
duplicate reads in Illumina short, single end reads of RNAseq data inbarpl Bioinformatics 4 05-22-2012 09:36 AM
TopHat pair-end RNAseq statistics Xiaomin Yu Bioinformatics 0 02-20-2012 09:02 AM
chip-seq read extension (36bp->200bp) vanbug Bioinformatics 5 01-30-2012 03:13 AM
Sequencing Illumina mate pair libraries beyond 36bp PNG Sample Prep / Library Generation 2 08-24-2010 12:54 PM
Running TopHat with 32bp or 36bp reads statsteam Bioinformatics 1 11-20-2009 07:55 PM

Thread Tools
Old 12-02-2012, 04:41 PM   #1
Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default Tophat RnaSeq(20-36bp)bp reads


I have 2 RnaSeq fq files that i need to analyze.i did the quality trimming and adapter trimming for the files as they were need to do it

then i got 2 output files that are 1.fq file(36 million bp reads) and 2.fq(40 million bp reads) with length of 20-36bp reads in it

I used tophat for aligning them to reference.then when i ran the tophat it is saying to decrease the --segment-length to half of the read length.

do i need to give the --segment-length to 18?or run with the default 25?

i need help in --coverage-search( when i used it in default it was saying that th e tophat will work slow if i used it)do i need to use the --no-coverage-search option for this?does it have any difference?

Please help me i am new in using the tophat

Thank you
abh is offline   Reply With Quote

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 06:41 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO