User: iraun
iraun • 3.8k
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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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Answer:
A: Quality check of NGS data
... Hey!
- For fastq quality control I would recommend the tradicional well known [FASTQC tool][1]
- For BAM, you can use as you mentioned, bamstat, or another alternative can be [Qualimap][2]
MultiQC can take the output of all of them and create a comprehensive report.
Another tool that I personall ...
written 3 months ago by
iraun • 3.8k
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Comment:
C: Ensembl ID mapping using Biomart
... [Here][1] you can find the answer to your first question about the decimal number in the Ensembl IDs.
[1]: https://m.ensembl.org/Help/Faq?id=488 ...
written 3 months ago by
iraun • 3.8k
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... Hello Biostars!
Let's assume that I have the 2 allelic versions of a given gene (Gene A). To be precise, I have previously characterised a heterozygous SNP on Gene A, and I've generated the 2 possible allele versions:
1. **Reference Gene A**: reference sequence (the SNP is not applied)
2. **SNP ...
written 4 months ago by
iraun • 3.8k
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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 8 months ago by
iraun • 3.8k
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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 8 months ago by
iraun • 3.8k
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5 follow
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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 ...
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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 3.5 years ago by
iraun • 3.8k
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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 3.5 years ago by
iraun • 3.8k
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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 3.5 years ago by
iraun • 3.8k
2
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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 3.5 years ago by
iraun • 3.8k
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For GATK: HaplotypeCaller gVCF and multisample
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For A: remove part of a multifasta header with sed or other
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For A: Bowtie2: Why won't it recognize my index files?
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