User: iraun

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iraun3.7k
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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

<prev • 375 results • page 1 of 38 • next >
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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 7 weeks ago by iraun3.7k
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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 7 weeks ago by iraun3.7k
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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 7 weeks ago by iraun3.7k
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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 2.9 years ago by iraun3.7k
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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 2.9 years ago by iraun3.7k
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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 2.9 years ago by iraun3.7k
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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 2.9 years ago by iraun3.7k
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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 iraun3.7k
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Comment: C: how to filter vcf file based on sample DP? vcf tools does not work
... 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 iraun3.7k
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Comment: C: Strand specific pair end sequencing
... [RSeQC infer_experiment.py][1] [1]: https://www.biostars.org/p/171298/#231982 ...
written 3.0 years ago by iraun3.7k

Latest awards to iraun

Appreciated 3 months ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: searching reads with a certain sequence in fastq file
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GATK: HaplotypeCaller gVCF and multisample
Appreciated 2.9 years ago, created a post with more than 5 votes. For samtools v1.3: AD, ADF and ADR fields.
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: Question about gens name starting "LOC~"
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: How to remove regions from a vcf file ?
Appreciated 2.9 years ago, created a post with more than 5 votes. For C: Why is it absolutely necessary to filter a VCF?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: GT and GL fields in VCF file
Great Question 2.9 years ago, created a question with more than 5,000 views. For GATK: HaplotypeCaller gVCF and multisample
Good Question 2.9 years ago, asked a question that was upvoted at least 5 times. For samtools v1.3: AD, ADF and ADR fields.
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Best software to assemble bacterial genomes
Good Answer 2.9 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 2.9 years ago, created an answer that was upvoted at least 5 times. For A: FPKM vs raw counts vs RPKM
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For C: Question about gens name starting "LOC~"
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: FPKM vs raw counts vs RPKM
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Get completely overlapping features
Popular Question 2.9 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 2.9 years ago, created a question with more than 1,000 views. For SGA: get the coordinates of contig scaffolding
Popular Question 2.9 years ago, created a question with more than 1,000 views. For samtools v1.3: AD, ADF and ADR fields.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Pindel: RPL structural variation type
Popular Question 2.9 years ago, created a question with more than 1,000 views. For scaffolding denovo contigs to genome
Popular Question 2.9 years ago, created a question with more than 1,000 views. For vcf-consensus with more than one alternative alleles
Popular Question 2.9 years ago, created a question with more than 1,000 views. For check the variations incorporated to consensus fasta by vcf-consensus
Popular Question 2.9 years ago, created a question with more than 1,000 views. For bwa.kit: run-bwamem or bwa mem
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Best software to assemble bacterial genomes

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