Forum: Bioinformatics
03-03-2020, 11:45 PM
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Replies: 2
Views: 870
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Forum: Bioinformatics
11-26-2019, 05:33 AM
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Replies: 10
Views: 2,235
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Forum: Bioinformatics
09-03-2019, 10:34 PM
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Replies: 3
Views: 1,106
Circadian cycle means the fluctuation follow a...
Circadian cycle means the fluctuation follow a cycle with a period (around) 24h... and in order to be efficient, it's better to have several periods of measurement...
I did my own scripts (it was...
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Forum: Bioinformatics
09-03-2019, 06:56 AM
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Replies: 3
Views: 1,106
Hi,
I actually did my PhD on circadian cycle...
Hi,
I actually did my PhD on circadian cycle (but on cyanobacteria).
I wrote some Rscripts by this time to calculate the period and phase of the circadian gene expression.
To be efficient, I had...
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Forum: Bioinformatics
03-26-2018, 05:37 AM
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Replies: 1
Views: 1,249
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...
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Forum: Bioinformatics
09-11-2017, 04:43 AM
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Replies: 4
Views: 2,585
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Forum: Bioinformatics
02-14-2017, 05:16 AM
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Replies: 4
Views: 1,237
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Forum: Pacific Biosciences
02-10-2017, 04:48 AM
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Replies: 7
Views: 2,906
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Forum: Illumina/Solexa
02-03-2017, 02:52 AM
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Replies: 14
Views: 4,436
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Forum: Illumina/Solexa
01-26-2017, 07:28 AM
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Replies: 17
Views: 2,642
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Forum: Illumina/Solexa
01-26-2017, 07:18 AM
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Replies: 17
Views: 2,642
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...
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Forum: Illumina/Solexa
01-26-2017, 07:12 AM
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Replies: 17
Views: 2,642
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Forum: Bioinformatics
01-12-2017, 10:11 PM
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Replies: 335
Views: 155,155
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...
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Forum: Bioinformatics
01-12-2017, 07:50 AM
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Replies: 335
Views: 155,155
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)
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Forum: Bioinformatics
01-12-2017, 06:55 AM
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Replies: 335
Views: 155,155
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Forum: Bioinformatics
01-12-2017, 06:36 AM
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Replies: 335
Views: 155,155
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Forum: Bioinformatics
01-12-2017, 06:19 AM
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Replies: 335
Views: 155,155
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Forum: Bioinformatics
01-12-2017, 05:17 AM
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Replies: 335
Views: 155,155
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Forum: Bioinformatics
10-07-2016, 01:50 AM
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Replies: 5
Views: 2,053
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Forum: Bioinformatics
10-06-2016, 12:48 AM
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Replies: 5
Views: 2,053
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Forum: RNA Sequencing
10-06-2016, 12:21 AM
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Replies: 5
Views: 1,829
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Forum: Bioinformatics
10-05-2016, 02:32 AM
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Replies: 0
Views: 816
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...
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Forum: Bioinformatics
08-30-2016, 05:38 AM
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Replies: 6
Views: 2,814
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Forum: Bioinformatics
07-21-2016, 07:49 AM
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Replies: 3
Views: 2,319
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...
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Forum: Bioinformatics
06-22-2016, 02:49 AM
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Replies: 2
Views: 2,338
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