User: arta

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arta0
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Posts by arta

<prev • 15 results • page 1 of 2 • next >
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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 11 days 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 21 days 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 26 days ago by arta0 • updated 26 days ago by Eric T.1.8k
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Comment: C: Counting number of duplicated reads for each gene or exon
... Great, thanks Pierre !!! ...
written 12 weeks 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 12 weeks ago by arta0 • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: HTseq or featureCounts without gff file
... Thanks Devon, I will look them. ...
written 3 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 3 months ago by arta0 • updated 3 months ago by Devon Ryan71k
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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 4 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 4 months ago by arta0
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How can i find the sequence of human domain ?
... Hey, I have done domain enrichment analysis and I got the significantly enriched domains from pfam. Now I would like to find the sequence of domains in human. Further I will align them for certain groups. But I could not find a source or database. Any help will be much appreciated. ...
domain database alignment written 4 months ago by arta0

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