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Search: Posts Made By: jordi
Forum: Oxford Nanopore 08-02-2017, 01:15 AM
Replies: 11
Views: 4,279
Posted By jordi
Hi @7tbear7, since you have MinION device, I...

Hi @7tbear7,
since you have MinION device, I am sure you have access to Nanopore Community. Look at the "Community-developed data-analysis tools" topic to find out which tools are devoted to deal...
Forum: Bioinformatics 01-26-2017, 07:51 AM
Replies: 2
Views: 1,638
Posted By jordi
Nanopolish without reference genome

Hi all!
I am trying to correct raw MinION sequencing reads with nanopolish since nanocorrect seems to be deprecated.
However, during the nanopolish workflow found here...
Forum: Oxford Nanopore 01-05-2017, 03:11 PM
Replies: 14
Views: 6,611
Posted By jordi
Hi Ola and wdecoster. Thank you very much for...

Hi Ola and wdecoster. Thank you very much for your answer, that was definitively helpful.
In the last point I meant the following: if there is no amplification step, how can I assembly a large...
Forum: Oxford Nanopore 01-04-2017, 01:26 AM
Replies: 14
Views: 6,611
Posted By jordi
Newbie MinION questions

Hi all!
I've some questions about Oxford nanopore Minion technology. I had a deep insight into the community of nanopore but I was unable to find out the answers:
1. What does it mean the "bps"...
Forum: Bioinformatics 05-25-2016, 06:11 AM
Replies: 4
Views: 874
Posted By jordi
Which commands did you use with Trinity and RSEM?

Which commands did you use with Trinity and RSEM?
Forum: Bioinformatics 01-13-2016, 04:38 AM
Replies: 5
Views: 906
Posted By jordi
:D Fantastic!!

:D Fantastic!!
Forum: Bioinformatics 01-13-2016, 04:20 AM
Replies: 5
Views: 906
Posted By jordi
Hi mastal and GenoMax, Thank you for your...

Hi mastal and GenoMax,
Thank you for your answers. It seems a bug from the perl script fastqFormatDetect.pl I used to predict the encoding system of my raw sequences since FASTQC and bbmap agree...
Forum: Bioinformatics 01-13-2016, 03:20 AM
Replies: 5
Views: 906
Posted By jordi
Quality encoding PE reads

Hi!
I am just checking the quality of a PE sequencing run. What I found it's a little bit tricky since from a PE reads, R1 seems to use a Phred33 encoding system whereas R2 is using a Phred64....
Forum: Bioinformatics 04-20-2015, 05:03 AM
Replies: 0
Views: 830
Posted By jordi
Illumina error profile

Dear all,
I am trying to reconstruct a known full length sequence from contig sequences obtained with Illumina. To do this I tried tblastn using a related sequence as a template.
Using that...
Forum: Bioinformatics 03-31-2015, 07:42 AM
Replies: 3
Views: 3,263
Posted By jordi
Update: using samtools depth I was unable to find...

Update: using samtools depth I was unable to find a position with 0 coverage. In fact it seems that I get the error message with rsem-parse-alignments since:

RSEM does not support gapped...
Forum: Bioinformatics 03-27-2015, 03:31 AM
Replies: 3
Views: 3,263
Posted By jordi
Hi gwilymh / all! I got the same error message....

Hi gwilymh / all!
I got the same error message. However I mapped reads back to transcripts using Bowtie2 allowing just the best alignment, as my reference transcriptome was a subset of filtered...
Forum: RNA Sequencing 02-13-2014, 04:13 AM
Replies: 4
Views: 4,747
Posted By jordi
Hi all! I am now dealing with this issue. I...

Hi all!
I am now dealing with this issue. I mean, how to determine chimeras in a RNA-Seq assembly without a reference transcriptome.
I've read that we are not able to tackle chimeras from different...
Forum: Bioinformatics 01-02-2014, 11:49 PM
Replies: 10
Views: 5,374
Posted By jordi
Hi, I found the same issue working with those...

Hi,
I found the same issue working with those data.
According to my opinion, setting a minimum read lenght should be included in he management of NGS data. However, I fix the problem using Trim...
Forum: Bioinformatics 11-14-2013, 08:36 AM
Replies: 6
Views: 1,689
Posted By jordi
Exactly! Older version....:mad: Thanks a lot...

Exactly!
Older version....:mad:
Thanks a lot ctseto!
However, I will let a chance to Trimmomatic again...:) thanks!
Forum: Bioinformatics 11-14-2013, 07:54 AM
Replies: 6
Views: 1,689
Posted By jordi
Hi ctseto! Thanks for your reply! I had a look...

Hi ctseto! Thanks for your reply!
I had a look to trimmomatic. However it didn't work as well as I expected. I mean, some primer sequences still remained in my fastq files.
That's what I decided...
Forum: Bioinformatics 11-14-2013, 07:38 AM
Replies: 6
Views: 1,689
Posted By jordi
fewer reads R1 than R2 bowtie2

Dear all,
perhaps I am going to ask something too much discussed. However I am absolutely unable to find the rigth answer. :(
Anyone knows how to perform a mapping step using Bowtie2 with a...
Forum: Bioinformatics 11-12-2013, 04:23 AM
Replies: 1
Views: 1,010
Posted By jordi
cutadapt

Hi all!
I'm using cutadapt in order to trim some files. Do you know if there is a specific way to pass an adaptor file to cutadapt options?? I mean, is there a way to avoid typing "-b sequence" many...
Forum: Bioinformatics 09-20-2013, 06:13 AM
Replies: 8
Views: 6,472
Posted By jordi
Hi all! No adapter trimming with sureSelect and...

Hi all!
No adapter trimming with sureSelect and good variant calling results.
However I've found what swNGS said regarding reverse complementary adaptor sequences resulting from amplicons shorter...
Forum: Bioinformatics 07-23-2013, 08:05 AM
Replies: 10
Views: 5,374
Posted By jordi
Thank you so much adamdeluca. That's is exactly...

Thank you so much adamdeluca. That's is exactly what I was looking for, a pair of sequences to be trimmed. I will try trimmomatic and cutadapt in order to find differences!
Forum: Bioinformatics 07-23-2013, 12:35 AM
Replies: 10
Views: 5,374
Posted By jordi
Trimming Haloplex adapters

Hi everyone!
I am trying to trim resulting amplicon reads from Haloplex and sequenced with MiSeq.
I've found some information :...
Forum: Bioinformatics 07-22-2013, 07:26 AM
Replies: 24
Views: 7,263
Posted By jordi
As far as I know using HaloPlex there are no 5'...

As far as I know using HaloPlex there are no 5' adapters. Reagrding 3' adapters there are a pair of seqeunces to be considered in the trimming step prior mapping the sequences:
>1...
Forum: Bioinformatics 01-11-2012, 07:54 AM
Replies: 4
Views: 1,487
Posted By jordi
Thank you westerman. You are right, that seems to...

Thank you westerman. You are right, that seems to be the right place to find out the solution, but what kind of reads it's going to be assembled?? I mean: in 454NewblerMetrics file you have assembled...
Forum: Bioinformatics 01-11-2012, 04:20 AM
Replies: 4
Views: 1,487
Posted By jordi
454 statistics

Hi all!
3 years ago we did a 454 run over a transcriptome data and using the Newbler release 1.1.03.24 we got some statistics in order to know the mean number of assembled reads per contig, the...
Forum: Bioinformatics 01-04-2012, 06:01 AM
Replies: 16
Views: 10,385
Posted By jordi
What about prinseq? ...

What about prinseq?
http://edwards.sdsu.edu/prinseq_beta/
Forum: Bioinformatics 01-03-2012, 01:05 AM
Replies: 0
Views: 1,551
Posted By jordi
GMAP vs TMAP

Hi all and happy new year!
Has anyone tried both programs in order to align some reads to a reference genome? Do you think one could compare each other according to their mapping-alignment...
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