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Tutorial:
Gene Set Enrichment Analysis
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Gordon
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written 3.5 years ago by
Hamid Ghaedi
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updated 6 days ago by
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Hagen
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written 10.2 years ago by
filipzembol
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Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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6 days ago by
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CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
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Recent Replies
Comment: different FeatureCounts output for the same data
by
GenoMax
141k
> featureCounts alignment rate is only around 15-20%.
You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
by
GenoMax
141k
> 20386810 (88.67%) aligned concordantly exactly 1 time
This result is fine.
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴
20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★
5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided.
tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
•
0
Hello,
you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport
cheers,
Comment: To get p-values for the TPM
by
VITALA
•
0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★
5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those.
DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
dsull
★
5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴
10
In my case , there is only one sample :
here is an example of a some variants generated using minipileup :
#CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
by
b.contreras.moreira
▴
170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴
40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴
20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1])
[1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
•
0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome.
[1]: https://www.na…
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