cortex_var

Sounds to me like your INDEX file is referring to a fastq/fasta file, not to a LIST of them Is that

Update. I moved the file to the wrong bin folder i think. after moving it to /usr/local/bin i no

I got the solution. I can't explain it very well. a colleague gave me the solution. for those

Of cause sorry about that. The link to the mailing list on https://github.com/mcveanlab/mccortex goes

Zam, you are right. the day after i send you a message i toke another look and saw the flaws in my

Both bc and pd Den lørdag den 1. april 2017 kl. 01.34.49 UTC+2 skrev Zamin Iqbal: Hi Mette It's a

Thank you! On Friday, March 31, 2017 at 5:32:18 PM UTC-6, Zamin Iqbal wrote: Sorry for the slow reply

It means zero read depth on both alleles.

Thanks Zamin! -r On Wednesday, 8 February 2017 09:20:19 UTC+8, Zamin Iqbal wrote: Apologies for the

Hi Zam there was indeed an issue with the index file. Now it went a step further, telling from the

Hi Zam While going over the files again, I found the logfile in the uncleanded binaries directory and

Cortex allows you to specify in advance how much memory to use. If this turns out to be not enough (

Hi I compiled cortex for K31 and 11 colours which worked fine Using the following command however

Hi Allison I think you need to get a unix person near you to help you follow Isaac's suggestions

Hi All I've moved all development of Cortex to github (https://github.com/iqbal-lab/cortex ).

Hi there >The four data files named mrsa0001_pe1, mrsa0001_pe2, cons00001_pe1 and cons0001_pe2 are

I've not tried very hard. In short kmer-based genotyping does work (see Mykrobe.com and nature.

Daniel Bad formatting for indel alleles: cct_C at ~/tools/cortex/CORTEX_release_v1.0.5.21//scripts/

Hi Joe As Cortex is involved in the analysis of genetic variation through de novo assembly, and with

Hi, I'm a newbie to Cortex_var and I've run into some confusion which I'm not sure how to

How many samples in total Ludo? In total, I have 60 samples. I have ran Trimmomatic again to remove

I'm looking forward to it! On Thu, Sep 10, 2015 at 1:33 PM, Zamin Iqbal <zam.iqbal.genome@

I'm pretty close to having something usable at the scales (10s of MB) that José is working with.

Hi Carlos, You asked me about this before and I forgot to reply, sorry. So, the purest way to do it

Hi! I would like to construct a graph from several similar reference genomes that I have. Then I

OK, well that command was almost identical to yours. Your error message was about reading a binary

Hi Winnie what is the error message in /faststorage/project/ClinicalMicrobio/05winnie/cortex/binaries

What do you mean lost 25% of your info. I think most likely the reason it thinks the LISTs of fastq

Can I just check - do you have new-lines/carriage returns at the end of those filelists? regards Zam

Duplicate of other email