Forum: Bioinformatics
01-24-2018, 12:31 PM
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Replies: 244
Views: 112,875
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Forum: RNA Sequencing
01-23-2018, 01:04 PM
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Replies: 5
Views: 2,070
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Forum: Bioinformatics
01-23-2018, 12:46 PM
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Replies: 244
Views: 112,875
@milan.molbio-
bbmap looks for the best...
@milan.molbio-
bbmap looks for the best alignment and reports only that one by default. If there are multiple "best" then you can get them all by setting 'ambig=all'.
What you're looking for...
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Forum: Bioinformatics
01-22-2018, 01:57 PM
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Replies: 244
Views: 112,875
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Forum: Bioinformatics
01-17-2018, 10:47 AM
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Replies: 9
Views: 15,276
I kinda take issue with both approaches. With...
I kinda take issue with both approaches. With alignment to genome I always miss some alignments because aligning RNA-Seq to the genome is relatively difficult. STAR misses some alignments that GSNAP...
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Forum: Bioinformatics
01-11-2018, 03:53 PM
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Replies: 678
Views: 214,794
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Forum: RNA Sequencing
01-11-2018, 03:22 PM
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Replies: 1
Views: 1,833
This locus looks like it has pretty low read...
This locus looks like it has pretty low read coverage based on the very blocky looking pileup. I'll say that a lot erratic coverage results from low read depth at a locus. Also if this is your first...
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Forum: RNA Sequencing
01-11-2018, 02:15 PM
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Replies: 1
Views: 2,803
I don't know any articles but it sounds to me...
I don't know any articles but it sounds to me like you're going to have to use these steps:
1. use the WGS to assemble the genome
2. align RNA-Seq to the assembled genome using an RNA-Seq aligner...
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Forum: RNA Sequencing
01-11-2018, 02:07 PM
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Replies: 2
Views: 2,287
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Forum: RNA Sequencing
01-11-2018, 01:51 PM
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Replies: 1
Views: 2,953
You may want to just split the data up into...
You may want to just split the data up into per-stimulation chunks. Otherwise the modeling in DESeq2 will use all samples and all stimulations to establish dispersions. If the separate stimulations...
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Forum: RNA Sequencing
01-11-2018, 01:44 PM
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Replies: 1
Views: 2,684
I'm interpreting your meaning of "transcript...
I'm interpreting your meaning of "transcript counts" to be the expression levels of transcripts. You're correct that those do appear in the individual assemblies however after merging, since the...
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Forum: RNA Sequencing
01-10-2018, 01:43 PM
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Replies: 1
Views: 3,533
Hi Jon,
Not sure if you're still after any...
Hi Jon,
Not sure if you're still after any kind of answer but I can contribute a little bit of experience that may help guide you.
Q1: sure it is!
Q2:
Not necessarily. Direct to...
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Forum: Bioinformatics
01-10-2018, 12:41 PM
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Replies: 1
Views: 2,078
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Forum: Bioinformatics
01-10-2018, 12:25 PM
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Replies: 2
Views: 3,077
I sometimes use bowtie2 for the alignment stage...
I sometimes use bowtie2 for the alignment stage of running RSEM (RNA-Seq gene expression). RSEM didn't allow INDELS in the alignments so as part of tweaking bowtie2 to not report those I was advised...
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Forum: Bioinformatics
01-10-2018, 10:17 AM
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Replies: 0
Views: 667
Is finding "all" alignments a pipe dream?
All is a bit arbitrary, of course, so maybe I just mean "all within a certain alignment quality boundary". I've wrestled with this time and time again - it seems that no matter how I tweak an...
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Forum: Bioinformatics
04-27-2017, 10:08 AM
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Replies: 678
Views: 214,794
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Forum: Bioinformatics
04-27-2017, 12:18 AM
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Replies: 2
Views: 1,392
first of all let me say that I agree with your...
first of all let me say that I agree with your interpretation. the third transcript does not overlap the first two and it has given all three the same 'gene_id' value.
the only thing that comes...
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Forum: RNA Sequencing
04-27-2017, 12:07 AM
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Replies: 6
Views: 7,347
farri-
Converting FPKM to TPM has zero...
farri-
Converting FPKM to TPM has zero effect on whatever careful way cufflinks calculated those FPKM values. It's actually not the FPKM that's carefully calculated within cufflinks but the...
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Forum: RNA Sequencing
04-26-2017, 11:52 PM
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Replies: 6
Views: 7,347
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Forum: Bioinformatics
04-26-2017, 11:42 PM
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Replies: 0
Views: 1,298
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Forum: Bioinformatics
04-26-2017, 10:43 PM
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Replies: 678
Views: 214,794
I was testing something with BBMap today and I...
I was testing something with BBMap today and I realized I had forgotten something about how to use it and couldn't figure it out. I was mapping RNA-Seq and I thought that it would report spliced...
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Forum: Epigenetics
12-10-2015, 07:29 AM
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Replies: 3
Views: 7,231
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Forum: Bioinformatics
07-23-2015, 12:56 PM
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Replies: 104
Views: 41,653
How does Tadpole compare to a short read...
How does Tadpole compare to a short read assembler such as Trinity? Is the output of Tadpole more like the results of the inchworm stage of the Trinity pipeline?
I tried Tadpole out on some...
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Forum: Bioinformatics
07-21-2015, 03:49 PM
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Replies: 678
Views: 214,794
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Forum: Bioinformatics
07-21-2015, 11:57 AM
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Replies: 5
Views: 3,053
Since it wasn't mentioned yet I'll add that...
Since it wasn't mentioned yet I'll add that cufflinks determines the strand of the assembled isoforms from the value of the XS attribute in the alignments (generated by STAR with --outSAMstrandField...
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