User: Kirill
Kirill • 260
- Reputation:
- 260
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- Location:
- Australia
- Twitter:
- kizza_a
- Last seen:
- 3 months ago
- Joined:
- 3 years, 11 months ago
- Email:
- k**************@monash.edu
Posts by Kirill
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Comment:
C: mm9 RNA-seq reference genome
... ```
wget ftp://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/dna/Mus_musculus.NCBIM37.67.dna_rm.toplevel.fa.gz
``` ...
written 6 months ago by
Kirill • 260
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... have a look at [varistran](https://github.com/MonashBioinformaticsPlatform/varistran) R package, specifically at
```
y <- varistran::vst(counts, design=design)
varistran::plot_heatmap(y, n=50)
``` ...
written 6 months ago by
Kirill • 260
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... edgeR uses replicates to estimates variability in your data. Your sources of variability are technical (usually small) and biological (usually much bigger). And what @WouterDeCoster is saying your estimate of variability will change by removing replicates, thereby altering downstream analysis. ...
written 6 months ago by
Kirill • 260
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... @gajkun I pretty much stopped (never really got to use) samtools mpile up. Mainly because it was slow and I found another (easier in my view) solution. Evgeniia (below) gave very good anwser on how to use samtools mpileup with bcftools. I don't do a lot of varinat calling, but when I do I mostly use ...
written 24 months ago by
Kirill • 260
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... Yes, this is exactly what I thought afterwards :) I did think I should count read towards both isoforms, but didn't know how to proceed from that.. I'll have look at Salmon sounds interesting.
...
written 3.3 years ago by
Kirill • 260
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... In featureCounts you can select "the range" to check against. For example you can set "the range" to be transcript coordinates. You can then you group by option to bin your reads into transcripts. You'd need to use `-t transcript` and `-g transcript_id`. I think (not too sure) you will also need to ...
written 3.3 years ago by
Kirill • 260
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... Hey NicoBxl,
I'm also doing per exon counts using featureCounts. This is the command I ran
featureCounts -T 14 -a my_gtf_file.gft -o my_output.txt -p -s 2 -g exon_id my_bam_file.bam
featureCounts v1.4.6-p2
And it worked for me.. (at least I think it did) I then manually collapsed all exons ...
written 3.3 years ago by
Kirill • 260
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... I know this isn't answering your question directly, but you can just supply your fastq files to the aligner, most aligners can merge them for you. I know that STAR does that for sure.
...
written 3.4 years ago by
Kirill • 260
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Comment:
C: txt file to bigwig
... to me wiggle file wouldn't be a good options, from what I understand wiggle file is good for representing something at a given genomic position, although position can span multiple bases.. I'm pretty sure you'll be better off investigating bed format and trying to convert your text file into bed, wh ...
written 3.4 years ago by
Kirill • 260
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... Hi there,
Just put them all in one fasta file. Here is note from the docs
fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc. The naming of the various sequences within this file determines how they are used. See the section below or use one of ...
written 3.4 years ago by
Kirill • 260
Latest awards to Kirill
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16 months ago,
created a question with more than 5,000 views.
For SAMtools mpileup and bcftools doesn't call InDels...
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Samtools mpileup quality scores all zero
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For SAMtools mpileup and bcftools doesn't call InDels...
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created a question with more than 1,000 views.
For GFFutils very slow at creating database file. Any Idea why..?
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2.5 years ago,
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For SAMtools mpileup and bcftools doesn't call InDels...
Popular Question
2.9 years ago,
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For SAMtools mpileup and bcftools doesn't call InDels...
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For SAMtools mpileup and bcftools doesn't call InDels...
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3.5 years ago,
created an answer with at least 3 up-votes.
For A: Samtools mpileup quality scores all zero
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3.8 years ago,
created an answer that has been accepted.
For A: Gff to fasta: Sort and extract sub-feature sequences from fasta in python
Teacher
3.8 years ago,
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For A: Samtools mpileup quality scores all zero
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3.8 years ago,
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For A: Gff to fasta: Sort and extract sub-feature sequences from fasta in python
Scholar
3.9 years ago,
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For A: Gff to fasta: Sort and extract sub-feature sequences from fasta in python
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