User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Answer: A: Read counts of STAR with gff file
... I have addressed this question to the developer of STAR, here is his answer if somebody is still interested https://groups.google.com/forum/#!searchin/rna-star/grant%7Csort:date/rna-star/yl6JRltAuG4/bbuKHQM4AgAJ ...
written 6 days ago by grant.hovhannisyan340
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Comment: C: Read counts of STAR with gff file
... If I don't provide the gff file STAR will not count anything, obviously because it does not have info about features. Also this is just a sample command, in real life I specify the path to gff. ...
written 6 days ago by grant.hovhannisyan340
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Comment: C: allelic specific expression with Kallisto
... Phased genome is a genome where two alternative haplotypes are distinguished. For example, in case of human with phased genome you would have both sequences from each of homologous chromosomes. Have a look at this review - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0762-6 Al ...
written 7 days ago by grant.hovhannisyan340
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Comment: C: allelic specific expression with Kallisto
... Do you have a phased genome? ...
written 8 days ago by grant.hovhannisyan340
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Comment: C: Cufflinks reports less transcripts then in gff
... Any previous exprerince with this issue? ...
written 9 days ago by grant.hovhannisyan340
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Cufflinks reports less transcripts then in gff
... Hi Biostars, To make transcriptome assembly, I mapped the reads (2x75, strand-specific, organism Candida albicans) with tophat2 and did assembly with cufflinks. The command line for the latter is `cufflinks --library-type fr-firststrand -o folder -g C_alb.gff -p 20 accepted_hits.bam` In final fi ...
cufflinks written 11 days ago by grant.hovhannisyan340
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Comment: C: Question on RNA-seq
... Regarding seq. depth, keep in mind 2 things. 1. If you will get bad quality sequencing you will have to do trimming, and depending on the read quality you might trim a substantial amount of data, thus decreasing your seq. depth. 2. For DE analysis what we are interested in are unique alignments to ...
written 6 weeks ago by grant.hovhannisyan340
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Answer: A: Question on RNA-seq
... This paper might be of interest https://academic.oup.com/bioinformatics/article/30/3/301/228651 And this is more broad https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8 ...
written 6 weeks ago by grant.hovhannisyan340
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Comment: C: simulate rnaseq reads from ref. genome
... Great, thank you both! ...
written 6 weeks ago by grant.hovhannisyan340
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Comment: C: simulate rnaseq reads from ref. genome
... Hi genomax, Thanks, and yes, basically I need reads from coding region to simulate RNAseq data. As far as I know, `randomreads.sh` generate reads from reference sequence, so in my case I'd have to extract transcriptome from genome and then feed it to `randomreads.sh`, is that correct? ...
written 6 weeks ago by grant.hovhannisyan340

Latest awards to grant.hovhannisyan

Supporter 4 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 6 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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