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Search: Posts Made By: SylvainL
Forum: Bioinformatics 03-26-2018, 04:37 AM
Replies: 1
Views: 510
Posted By SylvainL
Hi, with replicates for ChIPseq, the best would...

Hi,
with replicates for ChIPseq, the best would be to go with the ENCODE protocol (you can easily find with ENCODE ChIPseq guideline). They use IDR (Irreproducibility Discovery Rate), you can find...
Forum: Bioinformatics 09-11-2017, 03:43 AM
Replies: 4
Views: 861
Posted By SylvainL
Are you sure all these hits do not have the same...

Are you sure all these hits do not have the same score?
Forum: Bioinformatics 02-14-2017, 04:16 AM
Replies: 4
Views: 722
Posted By SylvainL
It will depend on the frame and orientation......

It will depend on the frame and orientation... You could make a short script extracting the nucleotides or the region (let's say 5 upstream and 5 downstream) and translate it yourself ...
Forum: Pacific Biosciences 02-10-2017, 03:48 AM
Replies: 7
Views: 1,303
Posted By SylvainL
Is it supposed to be a linear or circular genome?

Is it supposed to be a linear or circular genome?
Forum: Illumina/Solexa 02-03-2017, 01:52 AM
Replies: 14
Views: 2,565
Posted By SylvainL
I use this technique sometimes... Do not forget...

I use this technique sometimes... Do not forget to add some "N" at the beginning of your primers then, otherwise the colony detection may be inefficient (or you will have to spike PhiX at high...
Forum: Illumina/Solexa 01-26-2017, 06:28 AM
Replies: 17
Views: 2,003
Posted By SylvainL
:) I will be interested by the explanation then...

:)
I will be interested by the explanation then :)

I thought it could be a tagmentation followed by a Klenow repair which would keep the transposae "signature", but even like that, you wouldn't...
Forum: Illumina/Solexa 01-26-2017, 06:18 AM
Replies: 17
Views: 2,003
Posted By SylvainL
just to be sure I understood: the upper case...

just to be sure I understood: the upper case sequence is on the genome (meaning, it's really present in read1), while the problem concerns only the read2, so it's kind of inverted repeat on the...
Forum: Illumina/Solexa 01-26-2017, 06:12 AM
Replies: 17
Views: 2,003
Posted By SylvainL
Were the libraries prepared using tagmentation?

Were the libraries prepared using tagmentation?
Forum: Bioinformatics 01-12-2017, 09:11 PM
Replies: 307
Views: 83,759
Posted By SylvainL
Hi Brian, if I do NOT set maxlength=1, the...

Hi Brian,

if I do NOT set maxlength=1, the output is only reads shorter than 10 after trimming
if I set maxlength=1, I can get the normal output, i-e reads around 40-50bp after trimming...

I...
Forum: Bioinformatics 01-12-2017, 06:50 AM
Replies: 307
Views: 83,759
Posted By SylvainL
Ubuntu 12.04 server... :( java version...

Ubuntu 12.04 server... :(
java version "1.7.0_121"
OpenJDK Runtime Environment (IcedTea 2.6.8) (7u121-2.6.8-1ubuntu0.12.04.1)
OpenJDK 64-Bit Server VM (build 24.121-b00, mixed mode)
Forum: Bioinformatics 01-12-2017, 05:55 AM
Replies: 307
Views: 83,759
Posted By SylvainL
Ok, thanks for all this effort. I really don't...

Ok, thanks for all this effort. I really don't catch it. Now, it's running with maxlength=1 and I get the expected results.
Quite weird :)
Forum: Bioinformatics 01-12-2017, 05:36 AM
Replies: 307
Views: 83,759
Posted By SylvainL
I am using BBDuk version 36.84, I guess that's...

I am using BBDuk version 36.84, I guess that's the main difference...
Forum: Bioinformatics 01-12-2017, 05:19 AM
Replies: 307
Views: 83,759
Posted By SylvainL
Yes I know... As I edited, it works only if...

Yes I know...

As I edited, it works only if I set maxlength=1 !!

At least for the version I downloaded this morning ;)
Forum: Bioinformatics 01-12-2017, 04:17 AM
Replies: 307
Views: 83,759
Posted By SylvainL
Hi Brian, I also have a question. I downloaded...

Hi Brian,
I also have a question. I downloaded today the latest version of BBmap and I have a strange behaviour with left- and right-trimming

For example:...
Forum: Bioinformatics 10-07-2016, 12:50 AM
Replies: 5
Views: 1,087
Posted By SylvainL
Your replicates are paired (p1T, p1N, p2T, p2N,...

Your replicates are paired (p1T, p1N, p2T, p2N, etc...) so there is no need to split.
Forum: Bioinformatics 10-05-2016, 11:48 PM
Replies: 5
Views: 1,087
Posted By SylvainL
Hi dpryan, how slow for 1000 samples?

Hi dpryan,

how slow for 1000 samples?
Forum: RNA Sequencing 10-05-2016, 11:21 PM
Replies: 5
Views: 1,166
Posted By SylvainL
Sounds good to me... Over 70% of uniquely mapped...

Sounds good to me... Over 70% of uniquely mapped reads for Human is quite good. You also have to keep in mind that this percentage can obviously depend on the expressed genes...
Forum: Bioinformatics 10-05-2016, 01:32 AM
Replies: 0
Views: 560
Posted By SylvainL
Best tool to look for alterntive splicing

Dear all,

I would like to know which tools you use when you want to look for alternative splicing events.
Some goodies I am particularly looking for:
- works with either single or paired-end...
Forum: Bioinformatics 08-30-2016, 04:38 AM
Replies: 6
Views: 1,841
Posted By SylvainL
Actually, if the organism you work with is danio...

Actually, if the organism you work with is danio rerio (zebrafish), it may help to use paired-end even for single DE (a lot of duplications in this genome). For mouse or Humans, single-end are fine...
Forum: Bioinformatics 07-21-2016, 06:49 AM
Replies: 3
Views: 1,454
Posted By SylvainL
Using R... Ref_annotations is your gff file...

Using R...

Ref_annotations is your gff file you have to import using the function import.gff2 (with asRangedData=FALSE)
Ref_genome is your genome imported using read.DNAStringSet

The following...
Forum: Bioinformatics 06-22-2016, 01:49 AM
Replies: 2
Views: 2,038
Posted By SylvainL
Hi, it's an old thread but I have a comment... ...

Hi, it's an old thread but I have a comment...

I had to re-run the same pipeline on the same ChIPseqs using actually the ENCODE guideline and I am facing something I didn't expect: I do not get...
Forum: Bioinformatics 06-13-2016, 11:43 PM
Replies: 3
Views: 1,881
Posted By SylvainL
Since you did the mapping with STAR, it is...

Since you did the mapping with STAR, it is possible a read will be really long once mapped to the genome if it is at an exon-exon junction... You can use the parameter -split in your bedtools command...
Forum: Sample Prep / Library Generation 04-13-2016, 12:03 AM
Replies: 2
Views: 780
Posted By SylvainL
I am not sure I understand your point but I am...

I am not sure I understand your point but I am curious :)

Is it at the library prep step, using PCR? If yes, your material will (almost) double at each cycle, so your asumption is wrong. If it is...
Forum: Bioinformatics 04-11-2016, 11:33 PM
Replies: 2
Views: 604
Posted By SylvainL
Probably the best would be to see whether these...

Probably the best would be to see whether these tools exist in standalone version...
Forum: Bioinformatics 04-08-2016, 12:01 AM
Replies: 3
Views: 695
Posted By SylvainL
I would bet it does represent alignment between 2...

I would bet it does represent alignment between 2 sequences. In green, they are similar while in red it would be an inversion...

Do you know what it is and it's a game? Or not at all.... :)
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