SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mapping: how to deal not unique mapping to homologous genes in different contigs harlequin RNA Sequencing 0 08-26-2015 04:00 AM
mapping contigs to reference genome sadiexiaoyu Bioinformatics 2 07-04-2014 05:19 AM
Predicted Ensembl genes, but not in RefSeq sindrle RNA Sequencing 7 04-25-2014 08:24 AM
RNA-seq Mapping to Many Contigs Dario1984 Bioinformatics 10 06-26-2013 05:00 PM
Too few reads mapping back to contigs cerebralrust Bioinformatics 8 02-26-2012 10:25 PM

Reply
 
Thread Tools
Old 09-16-2019, 06:58 AM   #1
Drengo
Junior Member
 
Location: Europe

Join Date: Sep 2019
Posts: 1
Default Re-mapping contigs or predicted genes?

Hi!
I'm quite new to bioinformatics and am currently running into a dilemma on how to approach my re-mapping.
I have successfully assembled my FASTQ-files (reads) and now have my contigs in FASTA files.
From these FASTA-files, I want to predict its genes (with Prodigal) and find the depth (abundance) of the predicted genes. However, I am unsure if I should re-map my contigs back to my reads first, or if I should gene predict first, and then re-map the predicted genes back to the reads. As I see it, by re-mapping the predicted genes, I risk losing some of the reads not entirely in the gene. However, by re-mapping the contigs, I get a depth for all the reads on the contig, but will then have to correlate that data to the predicted genes somehow. Do you have any suggestions or preferences? And if you do, why would you choose one over the other.

Thank you very much in advance!
Drengo is offline   Reply With Quote
Old 09-16-2019, 09:37 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,978
Default

Cross-posted on biostars: https://www.biostars.org/p/398986/
GenoMax is offline   Reply With Quote
Reply

Tags
contigs, fasta, fastq, mapping, prodigal

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 05:03 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO