User: rthapa

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rthapa0
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Posts by rthapa

<prev • 40 results • page 1 of 4 • next >
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Comment: C: methylation coverage in the gene region
... Thank you for your reply. I went through methylkit package. I tried to read my file in but got an error. I am not sure what I am doing wrong. Could you please suggest? myobj = readBismarkCoverage( location = "/work/WGBS/methylkit",sample.id = "CHG_context_SRR5748817_1_bismark_bt2_pe.bed.gz.bism ...
written 17 days ago by rthapa0
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methylation coverage in the gene region
... Hi, I want to estimate the coverage of methylation in the gene-body region. I have coverage output from bismark. Chr05 241 241 100 9 0 Chr05 258 258 100 1 0 Chr05 260 260 88.8888888888889 8 1 Chr05 261 261 100 2 0 Chr05 263 263 88.8888888888889 8 1 Chr05 419 419 100 15 0 ...
methylation written 17 days ago by rthapa0
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Comment: C: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
... Could you try converting your text file to bed file using, awk -F"[:-]" 'BEGIN{ OFS="\t"; }{ print $1, $2, $3;}' bed.txt > bed.bed and then removing the space, sed 's/[[:space:]]*$//' input.bed > output.bed ...
written 24 days ago by rthapa0
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Answer: A: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
... You can try removing the extra space using; sed 's/[[:space:]]*$//' input.bed > output.bed ...
written 24 days ago by rthapa0
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codon adaptation index (CAI) estimation
... I am trying to get codon adaptation index score for all the fasta sequences. I have splitted the multifasta file to individual files with each fasta sequence. I tried to get CAI score using CAI python package and looping for each file. Although I could get scores result for some of my fasa files, af ...
codon usage written 25 days ago by rthapa0
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codon bias estimation (CAI)
... Hi, I am trying to find CAI values from cds sequences using CAI package in python. I am getting an error. Does anyone have suggestion? Thanks Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/CAI/CAI.py", line 204, in CAI sequence_weights.append(weig ...
protein written 26 days ago by rthapa0
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methylation coverage in the gene region
... Hi, I want to estimate the methylation coverage in the gene region. I have an output file from bismark. I would like to get the methylation coverage ( % of methylated cytosines/total cytosines) in the genomic region. I am not sure if methylpy can handle the output from bismark. Does anyone have sug ...
methylation written 28 days ago by rthapa0 • updated 28 days ago by ATpoint26k
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Comment: C: coverage of narrow peaks on genomic region using bedtools
... Thank you! that was a silly mistake. For some of the genes, I get the coverage as 1. But when I checked the start and end position of both peak output file and gene region file, I don't see 100 % coverage. Is the coverage not calculated as peak length/ gene length? ...
written 4 weeks ago by rthapa0
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coverage of narrow peaks on genomic region using bedtools
... Hi, I am trying to estimate the coverage of narrow peaks in genomic region. I have a bed file of both genomic coordinates and narrow peak output. When I use bedtools to find the coverage, all the results are 0 but by mere scanning of the peak region and genomic region, I can see some of the peak re ...
chip-seq written 4 weeks ago by rthapa0 • updated 4 weeks ago by Brice Sarver3.2k
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Comment: C: pysam alignment error
... thanks a lot, it finally worked. ...
written 5 weeks ago by rthapa0

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Popular Question 2 days ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 6 months ago, created a question with more than 1,000 views. For transcript count after string tie merge

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