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Search: Posts Made By: glacerda
Forum: Bioinformatics 07-13-2011, 06:16 AM
Replies: 2
Views: 3,792
Posted By glacerda
Use of illumina mate pair libraries for scaffolding

Hi colleagues,

I'm working with Illumina mate pair libraries and trying to use them for scaffolding. Illumina mate pair libraries have many problems that I believe that are not fully taken into...
Forum: Bioinformatics 05-19-2011, 10:35 AM
Replies: 13
Views: 4,123
Posted By glacerda
Hi xquan, Illumina mate pair libraries are...

Hi xquan,

Illumina mate pair libraries are supposed contain outwards facing reads ( <-- --> ) and we should use --rf in bowtie. Illumina Mate Pair libraries are used to long insert lengths,...
Forum: Bioinformatics 05-19-2011, 07:33 AM
Replies: 13
Views: 4,123
Posted By glacerda
The Illumina mate pair libraries used to be in...

The Illumina mate pair libraries used to be in reverse-forward orientation ( --rf parameter ), Unless something has changed in the mate pair protocol, this could be the cause of the bad mapping.
Forum: Bioinformatics 04-16-2011, 04:00 AM
Replies: 3
Views: 3,951
Posted By glacerda
Hi RLB_84, that's a very good question. In...

Hi RLB_84, that's a very good question.

In addition to the contig fasta files, Zorro takes as input the reads file (a subsample of WGS reads). The reads are used only to allow us to identify...
Forum: Bioinformatics 04-13-2011, 08:13 AM
Replies: 3
Views: 3,951
Posted By glacerda
Smile Zorro: The Masked Assembler (first public release)

ZORRO is an hybrid sequencing technology assembler. It takes 2 sets of pre-assembled contigs and merge them into a more contiguous and consistent assembly. We have already tested Zorro with Illumina...
Forum: Bioinformatics 04-01-2011, 07:22 AM
Replies: 0
Views: 1,349
Posted By glacerda
Exclamation mapping tool for resequencing

Hi colleagues,
Is there any mapping tool that can deal with Illumina mate pair libraries (3Kbp insert, outwards) with up to 50% of paired end 400bp insert inwards contaminating reads?
I would like...
Forum: Bioinformatics 02-22-2011, 11:17 AM
Replies: 1
Views: 3,463
Posted By glacerda
Question Going from FASTA scaffolds and FASTQ reads to AMOS BANK

Nowadays, most NGS assembly pipelines end in a scaffolds FASTA file. Typically, we have no assembly files (ace, contig, afg, among others). Thus, all we have to work is a scaffolds file (FASTA) and...
Forum: RNA Sequencing 10-21-2010, 04:07 PM
Replies: 1
Views: 2,509
Posted By glacerda
There are many programas for differential...

There are many programas for differential expression analysis in RNA-seq data. My favorites are edgeR and DEseq. Both are R packages, but they are well documented and easy to run, even for a R...
Forum: Bioinformatics 10-21-2010, 03:38 PM
Replies: 1
Views: 2,128
Posted By glacerda
k-gun12, the information you are looking for is...

k-gun12, the information you are looking for is on accepted_hits.sam and junctions.bed (fort the intron positions)

Youl could go from sam to wig using a sam2wig script you can find on the web (I...
Forum: RNA Sequencing 10-21-2010, 03:11 PM
Replies: 10
Views: 9,177
Posted By glacerda
Hi schmima, Thank you for commenting on this...

Hi schmima,

Thank you for commenting on this strategy. What you understood is exactly what I did. The whole Bedtools was used only to calculate IG-RPKM (what could be calculated in another way)
...
Forum: RNA Sequencing 10-20-2010, 10:40 AM
Replies: 10
Views: 9,177
Posted By glacerda
I have the same problem in some libraries. As I...

I have the same problem in some libraries. As I have not found any published and well stablished method to deal with that, I'm exploring some strategies.

For example, I can calculate the RPKM of...
Forum: Bioinformatics 10-07-2010, 10:14 AM
Replies: 7
Views: 3,340
Posted By glacerda
It is crucial to correct your reads prior to...

It is crucial to correct your reads prior to assembly (using the SOAPdenovo correction tool, SHREC or other). This will save memory in the assembly stage.

Last, SOAPdeNovo uses much less memory...
Forum: Bioinformatics 08-15-2010, 04:01 PM
Replies: 21
Views: 8,922
Posted By glacerda
nesoni samconsensus

Hi PFH, thank you very much for your help and for making this software package available for the community. The version 0.35 has solved the error I pointed, but there was another error in the...
Forum: Bioinformatics 08-12-2010, 01:43 PM
Replies: 21
Views: 8,922
Posted By glacerda
nesoni consensus error

Hi Torst, this tool looks very interesting.
I have tried to run "nesoni consensus" and it prints the following error messages. Do you know what is happening? It looks like there is a missing module,...
Forum: Bioinformatics 08-12-2010, 01:28 PM
Replies: 21
Views: 8,922
Posted By glacerda
removed...

removed...
Forum: Bioinformatics 08-04-2010, 03:54 PM
Replies: 0
Views: 2,766
Posted By glacerda
Scaffolding tool

Do you know any scaffolding tool targeted to NGS plattaforms? I am looking for something that can use contig fastas and aligned paired ends (eg SAM format) as input.

I know that most assemblers...
Forum: Bioinformatics 11-06-2008, 08:45 PM
Replies: 4
Views: 3,222
Posted By glacerda
edena and velvet are the best de novo assemblers,...

edena and velvet are the best de novo assemblers, however they were not designed to transcriptome data.

Be aware of the coverage bias os solexa technology. Regions of high GC have different (I...
Forum: Bioinformatics 11-06-2008, 08:38 PM
Replies: 8
Views: 4,323
Posted By glacerda
If possible, ask your sequencing provider to run...

If possible, ask your sequencing provider to run GS Reference mapper with your data. If it is not posible try nucmer+show-snps from the Mummer package
Forum: Bioinformatics 11-06-2008, 08:25 PM
Replies: 3
Views: 2,512
Posted By glacerda
This is Solexa, right? If it is, maybe you...

This is Solexa, right?
If it is, maybe you would like to look at that
maybe you would like to look at that:

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing....
Forum: 454 Pyrosequencing 11-06-2008, 08:13 PM
Replies: 2
Views: 2,749
Posted By glacerda
I have no idea of what is causing it, but short...

I have no idea of what is causing it, but short read lengths are typical of multiple templates in a bead. When this occurs, the sequence quality drops and the read is trimmed and is discarded or...
Forum: 454 Pyrosequencing 11-06-2008, 08:09 PM
Replies: 9
Views: 7,998
Posted By glacerda
I have compared a segment of 100K that we have...

I have compared a segment of 100K that we have sequenced by sanger (at > 20X) and by 454 ( > 50X)

Even at 50X, 454 made indel errors (all of them in homopolymers greater than 5 bp)

in you case,...
Forum: 454 Pyrosequencing 11-06-2008, 08:04 PM
Replies: 2
Views: 4,595
Posted By glacerda
I think that if you have a very high coverage...

I think that if you have a very high coverage Gbrowse won't be good. But if you test it and find it's ok, please tell us :) If you do, use the adaptor Bio DB SeqFeature Store (for versions of gbrowse...
Forum: 454 Pyrosequencing 11-06-2008, 07:58 PM
Replies: 3
Views: 2,943
Posted By glacerda
I am working with a 3K-LT run and I did not...

I am working with a 3K-LT run and I did not figure this problem before. Thanks for noticing that.
However, in my run, only 3% of the reads match a plasmid sequence.
Forum: 454 Pyrosequencing 11-06-2008, 07:55 PM
Replies: 4
Views: 3,875
Posted By glacerda
You could use cross_match to detect the 44mer...

You could use cross_match to detect the 44mer linker sequence and then use some perl to split the read into mates. Then you can use nucmer to map mates to the reference genome.

PS: I have noted...
Forum: Bioinformatics 08-06-2008, 09:52 PM
Replies: 6
Views: 6,045
Posted By glacerda
Thank you Mark, I will try this new pipeline as...

Thank you Mark, I will try this new pipeline as soon as it's released!

About comparing assemblies to a reference genome, I found a great utility in the Mummer package called dnadiff. It is a perl...
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