SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Running Deconseq Aishah RNA Sequencing 0 08-19-2019 07:52 AM
running CEGMA VM bioman1 Bioinformatics 1 09-08-2014 07:43 AM
KmerGenie output arthurmelo Bioinformatics 1 05-13-2013 12:14 AM
merging fastq running bwa gives different results from running bwa then merging sam. bw. Bioinformatics 1 06-25-2012 03:08 AM
tophat Error running running 'prep_reads' victoryhe Bioinformatics 2 10-17-2011 04:53 AM

Reply
 
Thread Tools
Old 08-20-2019, 06:30 PM   #1
fabio.marcelo
Junior Member
 
Location: Brazil

Join Date: Aug 2019
Posts: 1
Question Running kmergenie

Hello every one.
I'm new on bioinformatics. So, sorry if my question is too basic.
I'm trying to run kmergenie. It hasn't worked when I use reads_file.txt with the files I want to calculate the best k-mer. That's what I'm trying:
$ nano reads_file.txt
-> Paste:

../47G_mapped_1_val_1.fq
../47G_mapped_2_val_2.fq


$ kmergenie -l 21 -k 51 -s 5 reads_file.txt -o 47G_kmergenie

The message is:
running histogram estimation
File reads_file.txt starts with character ".", hence is interpreted as a list of file names
Reading 2 read files

End then it stops.
The only way kmergenie has worked is running one file at the time, but as I have paired end reads it's gonna take too long to finish the work.
Please can anybody help me?
fabio.marcelo is offline   Reply With Quote
Reply

Tags
kmer counting, kmergenie

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 06:16 AM.


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