SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
HISAT2: advantages of build index using annotated transcripts dekontrol Bioinformatics 0 06-22-2017 11:41 PM
Remove overlapping feature from GFF ruggedtextile Bioinformatics 1 06-20-2014 06:23 AM
remove overlapping PE reads RRBS shocker8786 Bioinformatics 1 01-22-2014 07:50 AM
MG-RAST - remove or retain non-overlapping paired-end reads rhinoceros Metagenomics 0 08-05-2013 05:31 AM
Cufflinks Annotated Transcripts magarolo RNA Sequencing 1 12-08-2011 02:34 AM

Reply
 
Thread Tools
Old 05-12-2020, 10:07 AM   #1
shaimaa
Junior Member
 
Location: uk

Join Date: May 2020
Posts: 1
Default How to remove transcripts overlapping with annotated genes

Hello,
Im trying to see the novel lnc RNA for not well annotated genome as very few lnRNA is known in this genome.
So what I'm doing is to align the fastq file with the whole genome fastafile to get the SAM file.
then annotate the SAM file with the stringtie and get the GTF file.
Now I want to remove this annotated transcript
What do you think?
and How to do it?
shaimaa 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 08:45 AM.


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