User: biplab

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biplab40
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Location:
University of California, Davis
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9 months, 1 week ago
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Posts by biplab

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How can I count read that falls into exon-intron and exon-exon junction?
... Thank you so much. I will try this. ...
written 20 days ago by biplab40
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How can I count read that falls into exon-intron and exon-exon junction?
... I have gtf file as follows VI ensembl gene 53260 54696 . - . gene_id "YFL039C"; gene_name "ACT1"; gene_source "ensembl"; gene_biotype "protein_coding"; VI ensembl transcript 53260 54696 . - . gene_id "YFL039C"; transcript_id "YFL039C"; gene_name "ACT1"; gene_source "ensembl"; gene_biotype ...
next-gen rna-seq sequencing written 8 weeks ago by biplab40 • updated 8 weeks ago by Alex Reynolds24k
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Comment: C: How to calculate distribution of mapped read over classes of RNA?
... That's true. Is there any option in bedtools to count only uniquely mapped reads? I did not find any. Then what is the best way to calculate percent of reads that aligned to genome but did not falls into any known features? ...
written 3 months ago by biplab40
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Comment: C: How to calculate distribution of mapped read over classes of RNA?
... Thank you so much. I used bedtools to calculate coverage over features. I got output like below for one feature in my gtf file. VII ensembl exon 437467 437934 . - . gene_id "YGL031C"; transcript_id "YGL031C"; exon_number "1"; gene_name "RPL24A"; gene_source "ensembl"; gene_biotype "protein_codi ...
written 3 months ago by biplab40 • updated 3 months ago by genomax51k
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How to calculate distribution of mapped read over classes of RNA?
... I am interested to find the percent of reads falls into mRNAs, snoRNAs, intergenic region etc. What is the best way to calculate percent of mapped reads falls into various classes of RNA as well as percent of reads that did not falls into any known features? Thank you so much ...
chip-seq rna-seq written 3 months ago by biplab40 • updated 12 weeks ago by debitboro80
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Comment: C: Why IVG coverage track from bam and bigwig files looks different?
... Thank you. This is how they look like. Seeing no coverage along rRNA, still does not make sense to me. Both tracks came from same bam file. ![link for igv track image][https://ibb.co/furfaS] ...
written 3 months ago by biplab40
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Why IVG coverage track from bam and bigwig files looks different?
... Hi I am studying polyadenylation of ribosomal RNA in different yeast mutants. I am interested in knowing how does the coverage of ribosomal RNA locus in my oligo-dT purified samples changes in various mutants. After alignment by HISAT2, I converted bam file to bigwig file by deeptools with a default ...
alignment next-gen rna-seq written 3 months ago by biplab40 • updated 3 months ago by dariober9.2k
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How can I use edgeR for comparing a lot of treatments with control with fewer lines of code to avoid error during contrasting?
... I am relatively new to R programming. I am using edgeR for differential expression analysis of my RNA-seq data. I have one control and around 25 treatments. I would like to compare contrast control with each treatment pair-wise. Currently I am doing it following way: c_vs_t1 <- glmLRT(fit, cont ...
R rna-seq written 4 months ago by biplab40
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Answer: A: HISAT2 running pair end
... I would try changing the file name to 'S1_F_paired_R1.fq' for R1 read and 'S1_F_paired_R2.fq' for R2 read. ...
written 6 months ago by biplab40
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Answer: A: Merging data coloum wise in R
... Read both files in R. Then use: merge(file1, file2, by='Gene', all=TRUE) ...
written 6 months ago by biplab40

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