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Search: Posts Made By: Pol8
Forum: Bioinformatics 08-06-2016, 12:25 PM
Replies: 1
Views: 1,233
Posted By Pol8
index bowtie2

Hi,

I get this error when running bowtie2-build:

Traceback (most recent call last):
File "/home/lab410/bin/bowtie2-build", line 26, in <module>
import logging
File...
Forum: Bioinformatics 03-17-2016, 01:42 PM
Replies: 1
Views: 769
Posted By Pol8
Python link error

Dear all,

I'm trying to install the ViennaRNA package, but got this error:

Could not link test program to Python. Maybe the main Python library has been
installed in some non-standard...
Forum: Bioinformatics 11-02-2015, 05:59 PM
Replies: 1
Views: 671
Posted By Pol8
pair reads visualization

Hi all,

is there a way in IGV (or other viewer) to visualize the pair reads, displaying each pair couple in a single line? I want to see how the two reads of each pair are far/close to each...
Forum: Bioinformatics 10-19-2015, 06:37 AM
Replies: 7
Views: 969
Posted By Pol8
Thanks, that works only for the first hit of my...

Thanks, that works only for the first hit of my fasta file. How can I do that for all the sequences?
Forum: Bioinformatics 10-18-2015, 12:49 PM
Replies: 7
Views: 969
Posted By Pol8
cut reads befor N

Hi,

I have reads with final Ns. Let's say, how can I get from this :

>R1
GGGGGGGTTTTTTTTTTTTTTTNT
>R2
GGGGGGGGGGTTTTTTTTTTNTTNT

to this (basically I want to cut the reads before the first...
Forum: Bioinformatics 10-16-2015, 06:04 PM
Replies: 1
Views: 706
Posted By Pol8
map with defined number of mismatches

Hi,

how can I map reads against the reference genome, so that I'm sure they align continuously, but allowing from 0 to 5 mismatches in the alignment?
Or alternatively find in the alignment,...
Forum: Bioinformatics 10-06-2015, 03:59 PM
Replies: 1
Views: 692
Posted By Pol8
software to estimate pair-end reads distance

Dear all,

is there a way to estimate if the distance among pair-end reads is higher or lower than expected, compared to the reference (and so, that there are deletions/insertions in the pair-end...
Forum: Bioinformatics 10-05-2015, 02:05 PM
Replies: 1
Views: 708
Posted By Pol8
split blast output based on evalues interval

Hi,

how can I split a blast ouput (outfmt 6) based on numeric range of evalues? Let's say I want to split it into two files: one with all the queries with evalues between 0 and 0.1, and the other...
Forum: Bioinformatics 07-29-2015, 05:44 PM
Replies: 0
Views: 497
Posted By Pol8
limit BLAST output

What's the difference between -max_target-seqs and num-alignments? I'd like to have only 1 alignment for each contig present in the query file
Forum: Bioinformatics 07-29-2015, 05:22 PM
Replies: 0
Views: 396
Posted By Pol8
MG-RAST sub-contigs

Hi,

how can I download, from my metagenome project, only the seqs (in FASTA format) that map against a specific phylum, e.g. viruses?
Forum: Bioinformatics 07-21-2015, 06:07 AM
Replies: 3
Views: 679
Posted By Pol8
I guess also hundreds of nt compared to the...

I guess also hundreds of nt compared to the reference, but it's just a speculation.. thanks
Forum: Bioinformatics 07-21-2015, 06:02 AM
Replies: 1
Views: 539
Posted By Pol8
on MIRA de novo

Hi,

I'm running MIRA for de novo sRNA assembly, but the contigs that I get are full of letters other than A,T,C,G. What's the problem?

Thanks
Forum: Bioinformatics 07-13-2015, 06:25 PM
Replies: 3
Views: 679
Posted By Pol8
map with gaps

How can I map sRNAs (20-30nt) to a reference, knowing that there are gaps in the sRNA?
Forum: Bioinformatics 07-13-2015, 02:50 PM
Replies: 2
Views: 807
Posted By Pol8
search CIGAR in SAM file

Hi,

how can I search a SAM file to find the alignments with N or D above a certain value in the CIGAR?
Forum: Bioinformatics 05-07-2015, 11:38 AM
Replies: 2
Views: 965
Posted By Pol8
filter contigs from fastq file

Hi,

I have a list of contig names. How can I filter those out from a FASTQ file to work on the left file?
Forum: Bioinformatics 03-03-2015, 05:10 AM
Replies: 2
Views: 711
Posted By Pol8
It works perfect!

It works perfect!
Forum: Bioinformatics 03-02-2015, 03:58 PM
Replies: 2
Views: 711
Posted By Pol8
filter above value

Hi,

I have a 3 columns file (conting name, lenght, number of reads).

How can I select the only contigs that are at least 500nt in lenght and that have at least 1000 reads mapping?

Is there a...
Forum: Bioinformatics 03-01-2015, 06:50 AM
Replies: 1
Views: 661
Posted By Pol8
Trinity: contigs vs reads

After obtaining the contigs, how can I know how many reads map to each contig?.. I want to have an idea of the abundance of the reads for each contig

Thanks
Forum: Bioinformatics 02-15-2015, 05:45 AM
Replies: 1
Views: 611
Posted By Pol8
sRNAs assembling

Hi,

which program(s) do you suggest to use for de novo assembling of sRNA reads 18-25 nt in lenght?

Thanks
Forum: Bioinformatics 01-28-2015, 02:58 PM
Replies: 1
Views: 1,339
Posted By Pol8
NCBI nr database

Hi,

I'm downloading the nr NCBI database. So I'll have my 28 folders. I decompress them.
Then, how can I launch a blastx against all the folders?

Thanks
Forum: Bioinformatics 01-27-2015, 05:22 AM
Replies: 3
Views: 1,206
Posted By Pol8
Great, thanks!!

Great, thanks!!
Forum: Bioinformatics 01-26-2015, 11:30 AM
Replies: 3
Views: 1,206
Posted By Pol8
NCBI taxid download

Hi,

how can I download all the sequences of a specific taxid from NCBI?

thanks
Forum: Bioinformatics 01-19-2015, 09:39 AM
Replies: 0
Views: 787
Posted By Pol8
TransDecoder

Hi,

what's the difference between the .mRNA and .cds output? THe .mRNA is not mentioned in the instructions.. (I think)

Thanks
Forum: Bioinformatics 01-17-2015, 05:52 AM
Replies: 1
Views: 833
Posted By Pol8
VelvetOptimiser

Hi,

I'm trying to use VelvetOptimiser, but get this;

..you may need to install the Bio::SeqIO module

What's the best source to install this module?
Thanks
Forum: Bioinformatics 01-16-2015, 07:09 AM
Replies: 1
Views: 774
Posted By Pol8
Velvet running?

Hi,

I launched Velvet but I don't know if it's still running. In the output folder I have 2 files: log (with the command line I gave) and Sequences (empty). I thik someting is wrong right?
...
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