User: iraun

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iraun3.8k
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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

<prev • 378 results • page 1 of 38 • next >
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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 4 days ago by iraun3.8k
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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 4 days ago by iraun3.8k
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Custom gene alleles + Kallisto for proxy Allele-specific expression analysis
... 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 ...
kallisto written 5 weeks ago by iraun3.8k
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Comment: C: Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... 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 4 months ago by iraun3.8k
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Comment: C: Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... 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 4 months ago by iraun3.8k
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Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
... 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 ...
kallisto rna-seq written 4 months ago by iraun3.8k • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... 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 3.2 years ago by iraun3.8k
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... 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 3.2 years ago by iraun3.8k
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Comment: C: HISAT2 and Stringtie: difference in Stringtie results when using pre-built index
... Sorry @Devon Ryan, my question wasn't clear. See my edit. I'm thinking that maybe the difference is not that big... ...
written 3.2 years ago by iraun3.8k
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HISAT2 and Stringtie: difference in Stringtie results when using pre-built indexes or creating new ones in HISAT2
... 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 ...
hisat2 written 3.2 years ago by iraun3.8k

Latest awards to iraun

Epic Question 5 weeks ago, created a question with more than 10,000 views. For GATK: HaplotypeCaller gVCF and multisample
Scholar 5 weeks ago, created an answer that has been accepted. For A: remove part of a multifasta header with sed or other
Scholar 5 weeks ago, created an answer that has been accepted. For A: Bowtie2: Why won't it recognize my index files?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: remove part of a multifasta header with sed or other
Appreciated 6 months ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Great Question 3.1 years ago, created a question with more than 5,000 views. For GATK: HaplotypeCaller gVCF and multisample
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: Why is it absolutely necessary to filter a VCF?
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: How to remove regions from a vcf file ?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Popular Question 3.1 years ago, created a question with more than 1,000 views. For samtools v1.3: AD, ADF and ADR fields.
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: GT and GL fields in VCF file
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: Question about gens name starting "LOC~"
Good Question 3.1 years ago, asked a question that was upvoted at least 5 times. For samtools v1.3: AD, ADF and ADR fields.
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: FPKM vs raw counts vs RPKM
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For C: searching reads with a certain sequence in fastq file
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Best software to assemble bacterial genomes
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For C: Question about gens name starting "LOC~"
Appreciated 3.1 years ago, created a post with more than 5 votes. For samtools v1.3: AD, ADF and ADR fields.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Get completely overlapping features
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How can I know if snp is inside a protein domain?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For SGA: get the coordinates of contig scaffolding
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: FPKM vs raw counts vs RPKM
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Pindel: RPL structural variation type
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Best software to assemble bacterial genomes

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