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Forum: Bioinformatics 02-10-2018, 08:48 AM
Replies: 0
Views: 463
Posted By frymor
Unhappy long noncoding RNA DE analysis

Hi everybody,

I am looking for a method/tool/workflow to analyse the differential expression of long ncRNA in C. elegans.
After searching the web for quite some time, I can't find a complete...
Forum: Bioinformatics 11-22-2017, 05:25 AM
Replies: 0
Views: 446
Posted By frymor
Pol III chip-seq experimental design

hi all,
we are planning on doing a ChIP-Seq experiment trying to identify PolIII binding sites in yeast and mouse.
As I am not really sure of the binding affinity of PolII I would like to ask for...
Forum: Bioinformatics 11-07-2017, 02:15 AM
Replies: 1
Views: 517
Posted By frymor
library depths for sequencing

Hi everybody,

I was approached by a biologist in our lab and was ask a specific question. As I was not really sure, I would like to share it with the community and hope to get some answers from...
Forum: Bioinformatics 06-28-2016, 05:11 AM
Replies: 1
Views: 796
Posted By frymor
I have solved the problem. no need of further...

I have solved the problem. no need of further info.
Forum: Bioinformatics 06-28-2016, 01:38 AM
Replies: 1
Views: 796
Posted By frymor
Fit for gene/exon XXX threw the next warning(s): restarting interrupted p

Hi,

I am running DEXseq on R 3.3 and get the following warning:

Fit for gene/exon ***** threw the next warning(s): restarting interrupted promise evaluation


for multiple (if not all)...
Forum: Bioinformatics 05-24-2016, 03:27 AM
Replies: 0
Views: 513
Posted By frymor
extending reads in ChIP-Seq analysis

Hi,

we're working on a ChIP-Seq data set. I have read in some tutorials and workflows that after mapping the reads, they should be extended to the estimated fragment size.

Am I correct in the...
Forum: Events / Conferences 05-02-2016, 12:32 AM
Replies: 2
Views: 1,432
Posted By frymor
I am truly sorry to have missed the webinar. Is...

I am truly sorry to have missed the webinar. Is it possible to download it, so that I can view it offline (when the internet connection is not so great)
Forum: Bioinformatics 04-12-2016, 10:52 AM
Replies: 1
Views: 1,782
Posted By frymor
hisat2 output more reads than are in the file

Hi all,
I am in the middle of testing the hisat2 mapper and encountered a discrepancy between the output hisat2 gives me at the end of the mapping step and the number of reads samtools flagstat...
Forum: Bioinformatics 04-06-2016, 03:16 AM
Replies: 0
Views: 1,139
Posted By frymor
running DEXSeq with hisat2 created bam files

Hi,

I am trying to run DEXSeq with bame files made by the hisat2 mapper. I have created the gff file according to the manual. I have seen that the chromosome names are different from the bam...
Forum: Bioinformatics 04-04-2016, 01:39 AM
Replies: 0
Views: 762
Posted By frymor
interpreting preseq results

Hi,

I am running the preseq c_curve and lc_extrap on a few fastq files using the option -V.
(Q: does it make sense at all to run preseq on the fastq files, or will it be more accurate, when...
Forum: Bioinformatics 03-10-2016, 11:34 PM
Replies: 2
Views: 2,348
Posted By frymor
yes I have seen that. I am trying to delete the...

yes I have seen that. I am trying to delete the post until I can recheck the results, but it was too late :o
Forum: Bioinformatics 03-10-2016, 11:27 PM
Replies: 2
Views: 2,348
Posted By frymor
Question Hisat2 vs. bowtie2 - why does bowtie2 mapped better?

Hi all,

I have 358 pairs pair-end samples from human genome. I am looking for the best way to map them to the reference for differential expression analysis.
I have tested the STAR aligner as...
Forum: Bioinformatics 11-27-2015, 04:31 AM
Replies: 2
Views: 1,521
Posted By frymor
sorry about spamming the forum. I have wanted to...

sorry about spamming the forum. I have wanted to delete the entries, but couldn't find any way to do so.
Forum: Bioinformatics 11-26-2015, 02:22 AM
Replies: 2
Views: 1,521
Posted By frymor
fastqc Exception (error)

Hi,

I am running the fastqc (v0.11.4) on Ubuntu 14.04.3 LTS.
I have four fastq files (two pairs of paired-end reads samples). They are AFAIK from old solexa machines in sanger format
somehow...
Forum: Bioinformatics 11-22-2015, 10:32 PM
Replies: 21
Views: 2,283
Posted By frymor
Hi Devon, you mentioned, being picky can be...

Hi Devon,

you mentioned, being picky can be a virtue, so I'm being picky again.

I was wondering about my first question for the comparison between the knock-out and the stimulation. I wanted...
Forum: Bioinformatics 11-18-2015, 01:59 AM
Replies: 7
Views: 1,663
Posted By frymor
yes, I thought this would be a problem. I have...

yes, I thought this would be a problem. I have removed the "unusual" falgs and it works perfectly.

thanks again
Forum: Bioinformatics 11-18-2015, 01:15 AM
Replies: 7
Views: 1,663
Posted By frymor
DEXSeq error with paired-end data

Hi,

I'm trying to run rhe python script for counting the reads for a dexseq analysis.
But I keep getting a strange error I can't understand

python...
Forum: Bioinformatics 11-18-2015, 12:25 AM
Replies: 21
Views: 2,283
Posted By frymor
Yes, it helps a lot. I think I start :(...

Yes, it helps a lot. I think I start :( understanding it.

I have another question about the colData. Does the order of the samples here must be the same as in the count table.
I am asking because...
Forum: Bioinformatics 11-17-2015, 07:47 AM
Replies: 21
Views: 2,283
Posted By frymor
Sorry to be so picky, but I still have some...

Sorry to be so picky, but I still have some difficulties understanding it, even if it might not seems this way.

What would be the difference between the two models:
~condition + stimulation
and...
Forum: Bioinformatics 11-17-2015, 05:08 AM
Replies: 21
Views: 2,283
Posted By frymor
thanks again, if I take one of the...

thanks again,



if I take one of the names from my resultNames() vector:
> resultsNames(dds)
[1] "Intercept" "condition_wildtype_vs_trippleKO"
[3]...
Forum: Bioinformatics 11-17-2015, 04:39 AM
Replies: 21
Views: 2,283
Posted By frymor
Hi all, thanks Devon for all the help. It...

Hi all,

thanks Devon for all the help. It seems to works quite good.

Just to make sure I have understood the way to create the multi-factor designs I was asked by a college of mine about a...
Forum: Bioinformatics 11-12-2015, 01:23 AM
Replies: 4
Views: 1,337
Posted By frymor
When calculating the pair-wise comparisons of the...

When calculating the pair-wise comparisons of the timepoints, does it make more sense to add the parameter test="Wald", or can I keep the LRT results?

I can see that there is a significant...
Forum: Bioinformatics 11-09-2015, 02:21 AM
Replies: 21
Views: 2,283
Posted By frymor
why shouldn't the biological replicates be...

why shouldn't the biological replicates be included in the model?

I haven't included the batch, because we don't see any batch effect when plotting a PCA. But i will try it with that two, when...
Forum: Bioinformatics 11-09-2015, 02:07 AM
Replies: 21
Views: 2,283
Posted By frymor
Post Now I am confused. "replica" are the biological...

Now I am confused. "replica" are the biological replica I have.:(

This is my colData:
sampleName hours replica batch
IFM_Myoblast_1 0 1 2014
IFM_Myoblast_2 0 2 2014
IFM_Myoblast_3 0 3 2014...
Forum: Bioinformatics 11-08-2015, 01:59 AM
Replies: 21
Views: 2,283
Posted By frymor
Thanks for the quick response. Maybe this is...

Thanks for the quick response.

Maybe this is a very basic statistical question, but to be honest I am not quite sure where is the difference :confused:

In this workflow I am trying to identify...
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