User: arta

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Posts by arta

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Job: Postdoc position in Bioinformatics at Karolinska Institute (Stockholm)
... Karolinska Institutet, Institutionen för onkologi-patologi, Forskargrupp Lehtiö At the Department of Oncology-Pathology basic, translational and clinical research and educational activities related to cancer is carried out. Approximately 300 people from over 40 nations are currently working at the ...
postdoc cancer job bioinformatics written 6 weeks ago by arta0
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Compare mus musculus and mus spretus genome structure annotation
... I would like to compare genome structure (gene models) annotation of *Mus Musculus* and Mus Spretus in terms of gene order, chromosome location etc... . So at the end i would like to come up how similar they are. I have both gtf files from Ensemble. I have checked that [link][1], but most of the l ...
gene model annotation written 9 weeks ago by arta0
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Comment: C: Error due to annotation file while running target module from CNVkit tool
... Sorry for the late reply, you were right. I needed to update the version of CNVkit. Thanks !!! ...
written 10 weeks ago by arta0
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Error due to annotation file while running target module from CNVkit tool
... Hi all, I am working on copy number alteration detection from exome sequencing (both tumor and normal samples) and using cnvkit package. I do have problem while i am preparing the BED file of baited regions. I am running following script and getting error. cnvkit.py target access-10kb.spretu ...
exome cnvkit cnv sequencing written 11 weeks ago by arta0 • updated 11 weeks ago by Eric T.1.9k
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Comment: C: Counting number of duplicated reads for each gene or exon
... Great, thanks Pierre !!! ...
written 4 months ago by arta0
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Counting number of duplicated reads for each gene or exon
... Hey, I am analyzing RNA-seq data and I am interested in duplicated reads. I know I can count number of duplicated reads overall using picard markDuplicates. > samtools view -f 1024 dedup_reads.bam | wc -l But i am interesting in the distribution of these duplicated. I have both sam and bam f ...
rna-seq written 4 months ago by arta0 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: HTseq or featureCounts without gff file
... Thanks Devon, I will look them. ...
written 5 months ago by arta0
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HTseq or featureCounts without gff file
... Hi, I am doing RNA-seq analysis for allele-specific gene expression. To do that, two mouse strains were hybrid. I do have reference fasta files for both but do no not have gff file for one strain. So far, I have done the mapping and alignment using STAR and I got **Aligned.sortedByCoord.out.bam* ...
next-gen rna-seq snp sequencing written 5 months ago by arta0 • updated 5 months ago by Devon Ryan73k
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Comment: C: How can i find the sequence of human domain ?
... There is no specific domain that i am referring. First it should be conserved among other species, (that is why they are called domain), second i have clusters of genes and the domains of the genes should enriched in given cluster. I have the domains for each clusters, now I would like to align them ...
written 6 months ago by arta0
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Comment: C: How can i find the sequence of human domain ?
... I meant 'protein sequence of domain'. ...
written 6 months ago by arta0

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Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to find genes that are involved in particular pathway ?

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