User: Kirill

gravatar for Kirill
Kirill270
Reputation:
270
Status:
Trusted
Location:
Australia
Twitter:
kizza_a
Last seen:
2 months, 3 weeks ago
Joined:
4 years, 8 months ago
Email:
k**************@monash.edu

Posts by Kirill

<prev • 51 results • page 1 of 6 • next >
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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 15 months ago by Kirill270
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Comment: C: How to create PCA plot and heatmaps using only significant genes in edgeR ?
... 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 15 months ago by Kirill270
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Comment: C: EdgeR analysis with different biological replicates numbers problem
... 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 15 months ago by Kirill270
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Comment: C: SAMtools mpileup and bcftools doesn't call InDels...
... @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 2.7 years ago by Kirill270
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Comment: C: featureCounts isoform vs gene summarization
... 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 4.0 years ago by Kirill270 • updated 4 days ago by RamRS25k
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Answer: A: featureCounts isoform vs gene summarization
... 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 4.0 years ago by Kirill270 • updated 5 days ago by RamRS25k
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Answer: A: featureCounts exon counting problem
... 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 exon ...
written 4.0 years ago by Kirill270 • updated 5 days ago by RamRS25k
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Comment: C: Observed and expected fastq header count different when merging two fastq files
... 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 4.1 years ago by Kirill270
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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 4.1 years ago by Kirill270 • updated 19 days ago by RamRS25k
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Answer: A: questions about TruSeq Adapter
... 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 on ...
written 4.1 years ago by Kirill270 • updated 19 days ago by RamRS25k

Latest awards to Kirill

Great Question 2.1 years ago, created a question with more than 5,000 views. For SAMtools mpileup and bcftools doesn't call InDels...
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Samtools mpileup quality scores all zero
Appreciated 2.7 years ago, created a post with more than 5 votes. For SAMtools mpileup and bcftools doesn't call InDels...
Popular Question 2.7 years ago, created a question with more than 1,000 views. For GFFutils very slow at creating database file. Any Idea why..?
Student 3.2 years ago, asked a question with at least 3 up-votes. For SAMtools mpileup and bcftools doesn't call InDels...
Popular Question 3.7 years ago, created a question with more than 1,000 views. For SAMtools mpileup and bcftools doesn't call InDels...
Popular Question 3.8 years ago, created a question with more than 1,000 views. For SAMtools mpileup and bcftools doesn't call InDels...
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Samtools mpileup quality scores all zero
Scholar 4.5 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 4.5 years ago, created an answer with at least 3 up-votes. For A: Samtools mpileup quality scores all zero
Scholar 4.5 years ago, created an answer that has been accepted. For A: Gff to fasta: Sort and extract sub-feature sequences from fasta in python
Scholar 4.6 years ago, created an answer that has been accepted. For A: Gff to fasta: Sort and extract sub-feature sequences from fasta in python

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