User: iraun
iraun • 3.7k
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PhD candidate at University of Oslo.
There is a distinct difference between having an open mind and having a hole in your head from which your brain leaks out. J. Randi
Posts by iraun
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... OMG... this is even more confusing, since Kaliisto author recommends using cDNA.. but if the file contains haplotypes.. I don't think it is the most sensible approach.. Let's see if the author drops by this issue or if another user has faced the same problem. At the moment I don't know anymore what ...
written 7 weeks ago by
iraun • 3.7k
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... Indeed, I totally agree about the misalignment risk. But kallisto authors recommend just to use cDNA, (see https://github.com/pachterlab/kallisto-transcriptome-indices/releases) so.. I am confused. ...
written 7 weeks ago by
iraun • 3.7k
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... Hi there!
I have run `kallisto` (version 0.43.1) twice, one run using the full human transcriptome (concatenating cDNA + ncRNAs into a fasta file) and another run using just cDNA sequences. Files were obtained from ensembl:
- cDNAs: ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/cdna/Homo ...
written 7 weeks ago by
iraun • 3.7k
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... Mmmm... Can you take a look to my second edit? Why using prebuilt indexes all the weight (expression) is given to `ENST00000462494` while using own indexes is given to `ENST00000331789`? ...
written 2.9 years ago by
iraun • 3.7k
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... Yes.
So the SNP and transcript information while building the index is "very" important? I mean, we assume that the analysis performed using `genome_snp_tran` index is better than the other? ...
written 2.9 years ago by
iraun • 3.7k
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... Sorry @Devon Ryan, my question wasn't clear. See my edit. I'm thinking that maybe the difference is not that big... ...
written 2.9 years ago by
iraun • 3.7k
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... Hello!
I'm using `HISAT2` tool for mapping a `RNA-Seq PE` dataset. The reference genome I want to align against is `GRCh37 `. I have downloaded [genome_snp_tran][1] pre-built index and run hisat2. For other hand, I tried to create my own indexes using the following command:
hisat2-build -p 6 ...
written 2.9 years ago by
iraun • 3.7k
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Comment:
C: extracting Allele Read Counts
... Depending on the variant caller you are using. For some of them you will see the following two fields under `FORMAT` column:
##FORMAT=
##FORMAT= ...
written 3.0 years ago by
iraun • 3.7k
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... You can take a look to this thread: [VCF filtering by depth][1]
For other hand, [SnpSift][2] is a great tool for filtering VCF files.
In your case the command would be:
`cat variants.vcf | java -jar SnpSift.jar filter "( DP > 10)" > filtered.vcf`
[1]: https://www.biostars.org/p/184457/
...
written 3.0 years ago by
iraun • 3.7k
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... [RSeQC infer_experiment.py][1]
[1]: https://www.biostars.org/p/171298/#231982 ...
written 3.0 years ago by
iraun • 3.7k
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