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Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 2 hours ago by
Ram
40k • written 9.9 years ago by
Irsan
★ 7.7k
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 5 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 19 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 years ago by
Luke Crichton
▴ 410
4
votes
2
replies
2.3k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 22 days ago by
GenoMax
134k • written 3.4 years ago by
ATpoint
77k
0
votes
1
reply
183
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 15 days ago by
ATpoint
77k • written 15 days ago by
JC
▴ 30
1
vote
0
replies
172
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 14 days ago by
Ram
40k • written 14 days ago by
Pierre Lindenbaum
157k
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Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
Comment: ncbi error report log for validate fastq issue
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Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
GenoMax
134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results
by
dsull
★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
Ram
40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
ATpoint
77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
by
Christopher
▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
Comment: ncbi error report log for validate fastq issue
by
GenoMax
134k
You may want to use `--split-files` instead. With your `--split-spot` option looks like you end up with interleaved data files. Unless you …
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
by
Ram
40k
Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
Comment: ncbi error report log for validate fastq issue
by
1769mkc
★ 1.1k
I got it working after i updated the sra lite option while using vdb-config -i the output is what i see like this docker run -t -…
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
by
camillab.
▴ 140
yeah but I am sure you know how to do it, whereas I am just go more confused :/
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
by
Ram
40k
Looks like we're on the same path
Comment: Mapping SNP rsIds/ positions to genes coding for proteins
by
Harsh
• 0
Actually the condition is, SNP should be within the gene boundary or 50kb upstream or 50kb downstream of the gene boundary.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
by
Ram
40k
Gotcha. Next time though, use RSEM as it internally uses STAR (as one option, it can use other aligners as well) anyway. Also, you're going…
Comment: Calculating TPM from featureCounts output
by
camillab.
▴ 140
Hi so I am confused I want to calculate the TPM from features counts and you wrote a very nice script but do I have to calculate the mean f…
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
by
camillab.
▴ 140
but I will have to align again the sample right? I struggled (a lot) to find a computer with enough RAM to run `STAR` and I I don't want to…
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
by
Ram
40k
Why not use something like RSEM to get counts *and* TPM?
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