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Forum: Bioinformatics 12-26-2017, 04:03 AM
Replies: 1
Views: 1,881
Posted By yvan.wenger
Background set for GO enrichment analysis

Hello,

I determined that out of ~70'000 transcripts, ~15'000 are spatially regulated (I used the LRT method in DESeq2). The patterns of these 15'000 transcripts clustered into 15 groups.

I...
Forum: Bioinformatics 12-18-2017, 11:28 AM
Replies: 1
Views: 1,739
Posted By yvan.wenger
GO analysis for non-mainstream species (using Panther annotation)

Hello,

I am sure this question has been asked many times, but so far I couldn't find a satisfactory answer to my question, so I am trying it here...

Most of the tools available use background...
Forum: De novo discovery 07-07-2016, 07:45 AM
Replies: 1
Views: 4,021
Posted By yvan.wenger
Ooops, I*should have had a more careful look....

Ooops, I*should have had a more careful look. While I*don't know what is exactly in the share/adapter.jf I*made my own:

../bin/jellyfish count -m 24 -s 5k -C -t 10 -o adapters_yvan.jf adapters.fa...
Forum: De novo discovery 07-07-2016, 07:20 AM
Replies: 1
Views: 4,021
Posted By yvan.wenger
MaSuRCA adapter trimming

Hello,

I am currently trying MaSuRCA, I get nice results but I think they can be further improved.

I made some test on a subset of reads, with or without clipping adapters before passing it to...
Forum: Bioinformatics 01-15-2014, 12:51 AM
Replies: 1
Views: 3,823
Posted By yvan.wenger
Hi BGould, Could you find a method in the...

Hi BGould,

Could you find a method in the end?

Best,

Yvan
Forum: Bioinformatics 12-09-2013, 08:21 AM
Replies: 1
Views: 1,184
Posted By yvan.wenger
Soft. to remove 5prime matches (to the left) from Illumina reads

Hello everybody,

My data contains trans-spliced leaders, i.e. short sequences that are attached to the 5 prime end of RNAs after transcription. In the organism I*use, there are about 15 of them...
Forum: Bioinformatics 07-18-2013, 04:36 AM
Replies: 0
Views: 1,064
Posted By yvan.wenger
Illumina reads pretreatmentS before de-novo transcriptome assembly

Hello everybody,

Lately with datasets of >1bio 100 bp SE reads, I have been using these steps to do de-novo assembly of a complex eukaryotic genome (without a good quality genome, diploid with a...
Forum: RNA Sequencing 06-11-2013, 10:44 PM
Replies: 1
Views: 1,906
Posted By yvan.wenger
Hi, Did you find out what was happening? Was...

Hi,

Did you find out what was happening? Was the low alignment rate indeed due to the FA treatment ?

Best,

Yvan
Forum: Bioinformatics 02-05-2013, 05:17 AM
Replies: 0
Views: 1,014
Posted By yvan.wenger
Bowtie not mapping (even) perfect matches ?

Hello everybody,

I am a little worried since about half of my reads do not align, although they have exact full-length matches in the my dataset.

I run bowtie with the command line:
...
Forum: Bioinformatics 11-16-2012, 02:53 AM
Replies: 0
Views: 1,564
Posted By yvan.wenger
Experimental design with edgeR and DESeq packages

Hi everybody,

I just started using edgeR and DESeq and am looking for a confirmation that I am not doing a silly thing.

Basically, we have 3 conditions and for only 1 of these sample we have...
Forum: RNA Sequencing 05-05-2011, 02:34 AM
Replies: 1
Views: 3,172
Posted By yvan.wenger
Newbler mapping: 50% chimeric reads?

Hello everybody,

I tried to map 454 reads on a genomic reference. I know the genome is not very good in term of contiguity (̃20'000 contigs). I*put below the mapping statistics. I*am a bit...
Forum: Bioinformatics 12-21-2010, 12:53 AM
Replies: 11
Views: 3,262
Posted By yvan.wenger
or maybe CTCAAAA-TCT ?

or maybe
CTCAAAA-TCT ?
Forum: Bioinformatics 12-20-2010, 02:01 PM
Replies: 11
Views: 3,262
Posted By yvan.wenger
Hello everybody, I also do no understand a...

Hello everybody,

I also do no understand a part of my pileup output (alignment generated with novoalign sam), maybe this is straightforward for somebody around? I would be very grateful if anybody...
Forum: 454 Pyrosequencing 12-06-2010, 11:35 PM
Replies: 2
Views: 1,503
Posted By yvan.wenger
Hello flxlex, I will try to be more clear....

Hello flxlex,

I will try to be more clear. First, the two pictures I attached come from two isotigs (out of a total of two), corresponding to a single gene. There are no other isotigs/isogroups...
Forum: 454 Pyrosequencing 12-06-2010, 06:16 AM
Replies: 2
Views: 1,503
Posted By yvan.wenger
Newbler sensitivity tuning for isoform detection?

Dear All,

I*performed an hybrid assembly with 454 Reads and Illumina-generated contigs (oases). I used the following command (mi 90, ml40 generated roughly the same output).

runAssembly -o...
Forum: 454 Pyrosequencing 12-03-2010, 08:28 AM
Replies: 2
Views: 3,222
Posted By yvan.wenger
Hello, I*am experiencing the exact same...

Hello,

I*am experiencing the exact same problem (cDNA, also MacPro, dual quad core, 32 Gb RAM on ubuntu). I did not have the problem with newbler 2.3.

The only difference is that the behaviour...
Forum: Bioinformatics 11-25-2010, 12:36 AM
Replies: 21
Views: 8,898
Posted By yvan.wenger
Hello Colin and pfh, Yes, thanks, that was...

Hello Colin and pfh,

Yes, thanks, that was the problem, I did not correctly added shrimp2 to my path...

Best,

Yvan
Forum: Bioinformatics 11-24-2010, 05:18 AM
Replies: 21
Views: 8,898
Posted By yvan.wenger
Hello everybody, I installed nesoni 0.4 but...

Hello everybody,

I installed nesoni 0.4 but get the following error when starting it with a test dataset: can anybody spot the mistake?

Best,

Yvan

>nesoni samshrimp nesoni_output crebs.fa...
Forum: Bioinformatics 11-24-2010, 03:47 AM
Replies: 3
Views: 3,200
Posted By yvan.wenger
454 Reads correction with Short reads ?

Hello everybody,

I can see that my 1Mio 454 reads are full of insertions/deletions in homopolymer regions, and of course this disrupts my ORFs in later stages (annotation step). Fortunately, I...
Forum: General 11-20-2010, 07:36 AM
Replies: 4
Views: 3,497
Posted By yvan.wenger
Hi, Of what I see these are standard names...

Hi,

Of what I see these are standard names for TF binding sites... I*just googled V$AP4_Q6 and find that http://www.broadinstitute.org/gsea/msigdb/cards/V$AP4_Q6.html

By any chance, did you...
Forum: Bioinformatics 11-20-2010, 07:30 AM
Replies: 0
Views: 1,132
Posted By yvan.wenger
free tool for gene model?

Hi everybody,

I'd like to map 454 (+illumina) reads to a genomic contig to get the splice variants possibilities.

It would be great if it could be linked to a visual interface resembling that:...
Forum: Bioinformatics 09-13-2010, 01:35 AM
Replies: 12
Views: 5,348
Posted By yvan.wenger
Hi everybody, I'd like to assemble a...

Hi everybody,

I'd like to assemble a transcriptome (a complex eukaryotic transcriptome)*de-novo and was wondering if somebody that already performed a similar assembly could give me a hint on an...
Forum: Bioinformatics 12-10-2009, 01:10 AM
Replies: 16
Views: 5,803
Posted By yvan.wenger
Update: I tried Ibis and it performed slightly...

Update: I tried Ibis and it performed slightly better than the GA Pipeline 1.4 on 3 lanes, ~60x10⁶ raw reads, 76 bp. Great tool. For the comparison I*tested raw reads (Ibis) vs raw reads (GAP).
...
Forum: Bioinformatics 12-09-2009, 07:05 AM
Replies: 23
Views: 24,811
Posted By yvan.wenger
Hello everybody, Some quick questions about...

Hello everybody,

Some quick questions about the topic, I number them as they are quite different from each other. Any input appreciated!

1. Can tophat/cufflinks be used with a de-novo...
Forum: Bioinformatics 12-02-2009, 02:24 AM
Replies: 83
Views: 289,211
Posted By yvan.wenger
paired-end and mate pairs

Paired-end and mate pairs. These two denominations refer to slightly different library preparations... correct?

Do we usually have the choice between the two? What are the practical differences...
Showing results 1 to 25 of 30

 


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