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Search: Posts Made By: Nicolas Nalpas
Forum: Bioinformatics 10-25-2013, 03:47 AM
Replies: 7
Views: 6,567
Posted By Nicolas Nalpas
Thanks for your answer Simon, I input my data...

Thanks for your answer Simon, I input my data into SeqMonk and it seems to work all right (I did follow the video instructions).
Also was I correct to input my BAM files (containing paired-end...
Forum: Bioinformatics 10-25-2013, 02:21 AM
Replies: 7
Views: 6,567
Posted By Nicolas Nalpas
Thanks for your answer Puggie. I am aware that I...

Thanks for your answer Puggie. I am aware that I may (must) have some contamination (even using strand-specific protocol), but since I do not have a spiked in in my samples it is impossible to...
Forum: Bioinformatics 10-24-2013, 08:47 AM
Replies: 7
Views: 6,567
Posted By Nicolas Nalpas
Hi everyone, I am also trying to identify...

Hi everyone,

I am also trying to identify antisense transcripts and quantify them.
My data are coming from cattle macrophages and have been prepared as paired-end strand-specific RNA-seq (using...
Forum: Bioinformatics 06-25-2013, 12:18 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, That is great, very helpful. ...

Dear Wei,

That is great, very helpful.
Thanks a lot.
Best wishes,
Nicolas
Forum: Bioinformatics 06-24-2013, 05:16 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, Really sorry to bother you again,...

Dear Wei,

Really sorry to bother you again, I have just one question as a matter of interest regarding featureCounts.

How do you handle your read count summarisation, when is a read assigned to...
Forum: Bioinformatics 06-20-2013, 12:59 AM
Replies: 218
Views: 146,534
Posted By Nicolas Nalpas
Dear Alex, I actually sorted it out by...

Dear Alex,

I actually sorted it out by reading again your previous answer, so I tried out with --genomeSAindexNbases to 7 and it seems to work fine now, no error so far.

Thanks again for all...
Forum: Bioinformatics 06-20-2013, 12:37 AM
Replies: 218
Views: 146,534
Posted By Nicolas Nalpas
Dear Alex, Thanks for your help, I have...

Dear Alex,

Thanks for your help, I have tried to generate my Mycobacterium bovis genome as you rocommanded:

STAR --runMode genomeGenerate --genomeDir...
Forum: Bioinformatics 06-19-2013, 11:18 AM
Replies: 218
Views: 146,534
Posted By Nicolas Nalpas
Hi everyone, At the moment, I am having an...

Hi everyone,

At the moment, I am having an issue with STAR 2.3.0e, which I am trying to use in order to align 2x90bases paired-end reads sample against Mycobacterium bovis genome NC_002945.3 from...
Forum: Bioinformatics 06-13-2013, 01:00 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, I have just tried the new version of...

Dear Wei,
I have just tried the new version of featureCounts, it works perfectly (see below).

## UNSTRANDED ## accepted_gene multi_mapping Notfound_gene Overlapped_genes
featureCounts with SAM...
Forum: Bioinformatics 06-12-2013, 06:15 AM
Replies: 218
Views: 146,534
Posted By Nicolas Nalpas
Dear Nino, That's great, thanks a lot for your...

Dear Nino,
That's great, thanks a lot for your answer.
It makes a lot of sense since I set up the alignment to output only uniquely mapping reads.
Thanks for the help.
Regards,
Nicolas
Forum: Bioinformatics 06-12-2013, 02:54 AM
Replies: 218
Views: 146,534
Posted By Nicolas Nalpas
Dear Alex, I am currently using STAR on a...

Dear Alex,

I am currently using STAR on a new strand-specific paired-end RNA-seq dataset, and I am very happy with the output.
I just have one question though (as a matter of interest really),...
Forum: Bioinformatics 06-12-2013, 12:31 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, Thanks for your reply. Enclosed...

Dear Wei,

Thanks for your reply.
Enclosed is a file containing my first 5,000 mapped reads (forgot to say in my earlier post that I used STAR to align my reads against Bos taurus 3.1.71 genome)....
Forum: Bioinformatics 06-11-2013, 09:15 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, We have now tried featureCounts...

Dear Wei,


We have now tried featureCounts v1.3.5-p1 to perform unstranded, stranded and reverse-stranded read counting on our new strand-specific dataset. While the unstranded parameter for...
Forum: Bioinformatics 06-02-2013, 04:41 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, This is great, thanks a lot for being...

Dear Wei,
This is great, thanks a lot for being so helpful and available.
I will give this a try on our dataset.
Thanks a lot.
Regards,
Nicolas
Forum: Bioinformatics 06-01-2013, 02:48 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, I just had another question about...

Dear Wei,

I just had another question about featureCounts and the strand specificity parameter.
We have a strand-specific RNA-seq dataset, on which we initially used HTseq-count, so as you know...
Forum: Bioinformatics 05-21-2013, 05:27 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Hi Wei, Thanks a lot for all your help,...

Hi Wei,

Thanks a lot for all your help, indeed it works perfectly now and so fast.
This is great.
Thanks again,
Nicolas
Forum: Bioinformatics 05-21-2013, 01:43 AM
Replies: 155
Views: 68,470
Posted By Nicolas Nalpas
Dear Wei, I was just wondering if you could...

Dear Wei,
I was just wondering if you could give advise on a featureCounts job that I tried to perform, I have RNA-seq data aligned to bovine genome (UMD3.1.71 from ENSEMBL) and I used...
Forum: Bioinformatics 01-11-2013, 03:50 AM
Replies: 11
Views: 6,487
Posted By Nicolas Nalpas
Hi GenoMax, Thanks a lot for your reply. ...

Hi GenoMax,

Thanks a lot for your reply.
For our RNA-seq experiment, our RNA-seq libraries were prepared using the epicentre (an Illumina company) ScriptSeq™ v2 RNA-Seq Library Preparation Kit...
Forum: Bioinformatics 01-11-2013, 02:38 AM
Replies: 11
Views: 6,487
Posted By Nicolas Nalpas
Hi wdt, I actually have the exact same...

Hi wdt,

I actually have the exact same question, just wondering if you got the answer to your question or if you are still looking?
If yes can you let me know the answer or where to find an...
Showing results 1 to 19 of 19

 


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