Forum: Bioinformatics
01-30-2018, 03:09 AM
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Replies: 104
Views: 41,784
Hi Brian,
After reading this whole thread,...
Hi Brian,
After reading this whole thread, I still have some doubts about how the mode=extend works in tadpole.
My understanding is: kmers of size k are extracted from the reads and, upon...
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Forum: Bioinformatics
03-03-2017, 04:44 AM
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Replies: 10
Views: 3,466
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Forum: Bioinformatics
11-10-2016, 05:13 AM
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Replies: 10
Views: 5,653
Hi,
I came to this post just now: I'm...
Hi,
I came to this post just now: I'm working on benthamiana too, calling variants and had the same question in my head. Since you asked this quite a time ago, maybe could you add up how you...
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Forum: Bioinformatics
11-10-2016, 02:35 AM
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Replies: 2
Views: 2,547
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Forum: Bioinformatics
10-31-2016, 08:08 AM
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Replies: 2
Views: 4,095
Hi, I know how.
First, quoting the...
Hi, I know how.
First, quoting the hisat2-align manual you will read that:
Since GFF / GTF files are usually prone to mis-formatting errors given that for a long time there has been no...
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Forum: Bioinformatics
10-31-2016, 06:45 AM
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Replies: 0
Views: 922
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Forum: Bioinformatics
08-24-2016, 12:49 AM
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Replies: 19
Views: 4,697
It looks like you still don't map more than 20%...
It looks like you still don't map more than 20% or your reads though... Maybe you didn't trim them correctly? How did you do the trimming process? Maybe they still contain some adapter sequences and...
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Forum: Bioinformatics
08-23-2016, 09:08 AM
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Replies: 19
Views: 4,697
I'm not sure about this. Because the...
I'm not sure about this. Because the supernumerarity itself doesn't affect the alignment if the sequence is the same for each supernumerary chromosome. If the sequence diverges, then you lose a lot...
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Forum: Bioinformatics
08-23-2016, 08:15 AM
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Replies: 19
Views: 4,697
I am surprised by the fact that bowtie2 maps ~...
I am surprised by the fact that bowtie2 maps ~ 70% of the data while bowtie maps only 45%. I think you should really make a list of all the parameters that bowtie2 applies by default and see which...
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Forum: Bioinformatics
08-23-2016, 01:33 AM
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Replies: 6
Views: 2,558
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Forum: Bioinformatics
08-23-2016, 01:27 AM
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Replies: 14
Views: 17,968
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Forum: Bioinformatics
08-23-2016, 01:22 AM
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Replies: 33
Views: 5,460
If you exported the RepeatScout-1 directory to...
If you exported the RepeatScout-1 directory to your $PATH, you don't need to write ./filename.prl, you just need to write filename.prl. If you include "./", it will search it in the current directory...
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Forum: Bioinformatics
08-23-2016, 01:12 AM
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Replies: 19
Views: 4,697
Before reaching out to the authors, I'd suggest...
Before reaching out to the authors, I'd suggest that you post here the BOWTIE command you ran (there must be somethign in the trinity log), to add info on the one from trinity you posted.
- How many...
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Forum: Bioinformatics
08-23-2016, 01:04 AM
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Replies: 2
Views: 2,334
Hey,
First, when you make and it throws out...
Hey,
First, when you make and it throws out warnings like unused-value, it doesn't mean that it automatically doesn't work (it can be). Sometimes these are warnings because some of the dependencies...
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Forum: Bioinformatics
08-17-2016, 06:28 AM
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Replies: 2
Views: 2,567
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Forum: Bioinformatics
08-17-2016, 06:15 AM
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Replies: 1
Views: 2,268
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Forum: Bioinformatics
08-04-2016, 04:21 AM
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Replies: 3
Views: 3,374
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Forum: Bioinformatics
08-04-2016, 04:12 AM
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Replies: 0
Views: 1,448
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Forum: Academic/Non-Profit Jobs
08-04-2016, 01:59 AM
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Replies: 0
Views: 1,226
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Forum: Bioinformatics
08-04-2016, 01:48 AM
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Replies: 3
Views: 3,374
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Forum: Bioinformatics
08-04-2016, 01:40 AM
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Replies: 1
Views: 2,631
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Forum: Bioinformatics
07-20-2016, 08:59 AM
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Replies: 3
Views: 3,374
BRAKER1 fails: inappropriate ioctl for device
Hi all, I'm having a problem which is more linux related than biology related. I'm running the BRAKER1 pipeline (which involves Augustus and Gene-mark ET) for a gene prediction, and I'm getting back...
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Forum: RNA Sequencing
07-20-2016, 08:51 AM
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Replies: 2
Views: 1,448
Totally agree. Using FPKM or RPKM in this case...
Totally agree. Using FPKM or RPKM in this case can be done because cufflinks outputs it automatically in the isoforms.fpkm_tracking file so you don't bother using other units.
What you need is to...
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Forum: Bioinformatics
07-20-2016, 08:33 AM
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Replies: 2
Views: 2,640
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Forum: Illumina/Solexa
07-20-2016, 08:19 AM
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Replies: 2
Views: 1,291
Before merging them I would go with some...
Before merging them I would go with some statistical test to see their closeness. For example, run cufflinks on both separately and then do a principal component analysis (PCA) with R to see how...
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