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Search: Posts Made By: punto_c
Forum: Bioinformatics 12-03-2014, 07:06 AM
Replies: 12
Views: 6,352
Posted By punto_c
Thank a lot...

Hello Brian

I had the same error from bwa mem, but I found out the reason was the sorting of the reads.

I solved the problem using your tool repair.sh in bbtools,
that was just great and...
Forum: Bioinformatics 08-06-2014, 05:56 PM
Replies: 4
Views: 1,387
Posted By punto_c
Prodigal contains the option for predicting ORF...

Prodigal
contains the option for predicting ORF in contigs from metagenomic data
in all the cases you will have to assemble (or try to) the reads

do you know if in the list you suggested there...
Forum: Bioinformatics 06-04-2014, 07:01 PM
Replies: 657
Views: 137,863
Posted By punto_c
thank you

Thank you a lot Brian
Your explanation was as always very simple and clear
I could trimm in PE mode using Cutadapt and then was able to map the reads
Nothing to do for Fastx

thanks again
...
Forum: Bioinformatics 06-04-2014, 01:54 AM
Replies: 657
Views: 137,863
Posted By punto_c
Hello Brian I am trying to compare some...

Hello Brian

I am trying to compare some mapping tools, and I am also using BBMap
I execute 4 tests using PE readed preprocessed with bbduck, cutadapt, fastx and trimmomatic respectively
With the...
Forum: Bioinformatics 06-02-2014, 05:35 PM
Replies: 308
Views: 86,052
Posted By punto_c
Hello Brian Thank you for your reply Actually...

Hello Brian
Thank you for your reply
Actually I realised the copies were there just after I posted my question
anyway it was not clear to me that only n-1 of the copies goes to the file specified...
Forum: Bioinformatics 06-02-2014, 02:59 AM
Replies: 308
Views: 86,052
Posted By punto_c
Hello Brian sorry if I write on the wrong...

Hello Brian

sorry if I write on the wrong post, but I wanted to ask you about dedupe
I wanted to know if it possible to output simple stats about the repeated sequences
For example:
number of...
Forum: Bioinformatics 05-27-2014, 12:40 AM
Replies: 308
Views: 86,052
Posted By punto_c
Ciao Thank you a lot for your nice and fast...

Ciao

Thank you a lot for your nice and fast reply
I wanted to inform you that based on my first simple tests on illumina data your method performed best, followed closely by trimmomatic
the...
Forum: Bioinformatics 05-20-2014, 08:10 PM
Replies: 308
Views: 86,052
Posted By punto_c
Hello Brian First of all thank you for sharing...

Hello Brian
First of all thank you for sharing your software
I am currently testing a few reads preprocessing tools (cutadapt, trimmomatic, fastx_tools and BBmap)

I can see from your post that...
Forum: Bioinformatics 05-20-2014, 08:08 PM
Replies: 308
Views: 86,052
Posted By punto_c
PE adapter trimming in single command

Hello Brian
First of all thank you for sharing your software
I am currently testing a few reads preprocessing tools (cutadapt, trimmomatic, fastx_tools and BBmap)

I can see from your post that...
Forum: Bioinformatics 05-16-2014, 11:22 PM
Replies: 4
Views: 1,626
Posted By punto_c
Thank you Mchicken, yes I know my adapters, I am...

Thank you Mchicken, yes I know my adapters, I am just considering thepossibility to automate the process for an high level software that could be used by clinitians.
So I would like to find a way to...
Forum: Bioinformatics 05-16-2014, 01:36 AM
Replies: 4
Views: 1,626
Posted By punto_c
Automatic adapter identification for trimming

Hello everybody,

I am kind of new ot the analysis of NGS data, so I am sorry if my questions
my be to simple, or not easy to understand

I was wondering if there is any software (or in-house...
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