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Search: Posts Made By: Pepe
Forum: Bioinformatics 08-09-2014, 10:14 AM
Replies: 13
Views: 5,332
Posted By Pepe
Hi all, I am not sure if Marevilla and...

Hi all,

I am not sure if Marevilla and Ayush_Saxena are still interested, or if the developers are around.
I was having the same problem as some of you:
I run CNVseq for multiple bam files and...
Forum: SOLiD 03-03-2011, 10:21 PM
Replies: 11
Views: 3,637
Posted By Pepe
10x is very little sequencing for a de novo...

10x is very little sequencing for a de novo project.
Also, consider normalization of your samples to obtain even coverage the transcripts.
Prices depend on the facility where you sequence. Having...
Forum: Bioinformatics 02-26-2011, 03:10 PM
Replies: 2
Views: 1,591
Posted By Pepe
You'll find matches for eads belonging to places...

You'll find matches for eads belonging to places outside your partial genomic reference. Mapping algorithms try to find the best hit in the reference provided. If the real place is not provided...
Forum: Sample Prep / Library Generation 02-10-2011, 07:08 AM
Replies: 5
Views: 10,038
Posted By Pepe
Thanks for your reply. We have decided to do...

Thanks for your reply.
We have decided to do the same, the hope is that we can integrate the new Truseq kits (high throughput) and the dUTP methods (best quality according to Levin et al.).
...
Forum: Sample Prep / Library Generation 02-09-2011, 08:16 AM
Replies: 5
Views: 10,038
Posted By Pepe
strand specific RNAseq

Hi all,

I am interested in hearing from users preparing strand-specific RNAseq libraries. We work with plants.

We are considering the ScriptSeq kit, but we are not sure about how well does it...
Forum: Bioinformatics 10-08-2010, 03:41 PM
Replies: 23
Views: 23,268
Posted By Pepe
This thread contains a perl script to get reads...

This thread contains a perl script to get reads that are in a .fq file but not in a sam file. It was written with TopHat in mind but it may work for you too.
I'm not sure if it helps. ...
Forum: Illumina/Solexa 10-08-2010, 03:23 PM
Replies: 9
Views: 6,750
Posted By Pepe
What i do with my paired end reads is to filter...

What i do with my paired end reads is to filter out the ones that have adapters or bad quality. Then I take the pairs of the removed ones and I put them in a separate file, so the 2 paired end files...
Forum: Bioinformatics 06-20-2010, 09:43 AM
Replies: 5
Views: 6,929
Posted By Pepe
What do ti and tv stand for?

What do ti and tv stand for?
Forum: Bioinformatics 05-31-2010, 10:33 PM
Replies: 0
Views: 2,043
Posted By Pepe
Tophat --segment-length

Hi,

I hope the developers see this post. I'll post it here so I can attach a figure that will help me making my point.
I think I've found a bug in Tophat (v1.0.13).

Reads that are spliced in...
Forum: Bioinformatics 05-20-2010, 07:06 AM
Replies: 3
Views: 9,032
Posted By Pepe
If the organism that you are sequencing has a...

If the organism that you are sequencing has a deletion in comparison with the reference, the gapped aligner will do something like:


read: ATGAT-ATGATGA
ref: ATGATGATGATGA


Aligners that do...
Forum: Bioinformatics 05-17-2010, 08:57 AM
Replies: 5
Views: 8,242
Posted By Pepe
You cannot open a file in Pileup format with...

You cannot open a file in Pileup format with Bio::DB::sam

You should convert your SAM file to BAM format (samtools view) and sort it (samtools sort), maybe index it too? I'm not sure (samtools...
Forum: Bioinformatics 04-24-2010, 11:10 PM
Replies: 7
Views: 5,262
Posted By Pepe
I haven't used SOAP, but I found once a software...

I haven't used SOAP, but I found once a software that did not like numbers as fasta headers.
Forum: Bioinformatics 02-23-2010, 10:03 PM
Replies: 5
Views: 4,376
Posted By Pepe
In any case, the ShortRead package in R will...

In any case, the ShortRead package in R will solve your trimming problems.
You'll need to know/learn R though.
Here there are very useful examples on how to do the trimming and much more:...
Forum: Bioinformatics 01-17-2010, 07:11 PM
Replies: 3
Views: 5,852
Posted By Pepe
Hi, commas and periods represent reads with...

Hi,

commas and periods represent reads with nucleotides that match the reference, that's why it says you have 31 of them.

I'm not sure about the **.
Forum: Bioinformatics 01-12-2010, 09:55 PM
Replies: 1
Views: 3,269
Posted By Pepe
TopHat coverage.wig file wish list

Hi,

I wanted to add to the list of things to have into account for the next version of TopHat, in case the developers are around.
I'm using Tophat v1.0.12 and Bowtie v0.11.3
I noticed that the...
Forum: Bioinformatics 12-17-2009, 06:30 PM
Replies: 1
Views: 4,165
Posted By Pepe
Bimodal insert size distribution

Hi,

we have used the RNAseq Illumina protocol to make about a dozen paired-end libraries.

Once sequenced and aligned to the reference genome I plot the distribution of insert sizes and I see a...
Forum: Bioinformatics 12-13-2009, 07:35 AM
Replies: 6
Views: 5,011
Posted By Pepe
You need to read the sam format specifications: ...

You need to read the sam format specifications:
Look it up on google.
Column number 9 is the Inferred insert SIZE (ISIZE). If all of those in your file are 0, then you have single ends (or no read...
Forum: Illumina/Solexa 12-02-2009, 03:26 PM
Replies: 9
Views: 85,799
Posted By Pepe
Here's what the person that did this replied:

Here's what the person that did this replied:
Forum: Illumina/Solexa 11-23-2009, 09:09 AM
Replies: 9
Views: 85,799
Posted By Pepe
Thanks Simon, We are now running 8 samples...

Thanks Simon,

We are now running 8 samples per lane and we don't see many more purity filter losses compared to when we did not use barcodes.
I have been a very interested observer in the the...
Forum: Bioinformatics 09-17-2009, 07:11 AM
Replies: 12
Views: 6,854
Posted By Pepe
I saw this the other day: ...

I saw this the other day:

http://www.tgen.org/mged/index.cfm

Although it looks more in the bioinformatics side than on the 'pure' biologist side.
Forum: Illumina/Solexa 09-11-2009, 03:07 PM
Replies: 9
Views: 6,405
Posted By Pepe
I don't think you want to pool them back since it...

I don't think you want to pool them back since it makes a big difference to know the approximate distance between paired reads when aligning or assembling.
If you pool them you loose that advantage.
Forum: RNA Sequencing 09-11-2009, 03:00 PM
Replies: 9
Views: 12,400
Posted By Pepe
You can't use Bowtie without a reference genome....

You can't use Bowtie without a reference genome. But there are others that can (Velvet, etc.)... just search for them in this forum...
Forum: Illumina/Solexa 08-19-2009, 10:35 AM
Replies: 9
Views: 85,799
Posted By Pepe
Question Barcoded PE adapters for multiplexing up to 12 samples

Hi all,

We would like to ask your opinion on this issue. I'm sure that people is more used to thinking about this than we are.
We are designing our own barcodes so they are as short as possible....
Forum: General 05-27-2009, 07:48 AM
Replies: 5
Views: 6,293
Posted By Pepe
Having orientation does not seem very important...

Having orientation does not seem very important because most experiments don't have the ability to see it. I bet there are many interesting surprises once it becomes a standard.
For example, I've...
Forum: Bioinformatics 05-18-2009, 07:41 PM
Replies: 5
Views: 4,322
Posted By Pepe
For question A: ...

For question A:
http://www.nature.com/nbt/journal/v27/n5/abs/nbt0509-455.html
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