User: DL

gravatar for DL
DL10
Reputation:
10
Status:
New User
Location:
India
Last seen:
1 week, 3 days ago
Joined:
3 years, 3 months ago
Email:
l**************@gmail.com

Posts by DL

<prev • 52 results • page 1 of 6 • next >
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Comment: C: Regarding Bamstat05 output
... Thank you for your reply. I see -f option but i did not understand how can i run command with -f option if i want to take only those reads that mapped less than 10 times. because i want to calculate coverage mapped reads on transposable elements so i gave bed file for TE and bam file after mapping ...
written 12 days ago by DL10
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Comment: C: Regarding Bamstat05 output
... Thank you for your reply . Regards ...
written 12 days ago by DL10
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Comment: C: Regarding Bamstat5 output
... Thank you for your reply. If i understand well then coverage is depth that mention how many reads are aligned at that particular position and in my table it showed zero. Its mean that no reads are aligned at some positions. Thank you ...
written 12 days ago by DL10
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Comment: C: Regarding Bamstat5 output
... Ok, i will remember next time. Thank you ...
written 12 days ago by DL10
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Regarding Bamstat05 output
... Hello, I ran [bamstats05][1] to check the coverage from bam file. Can anyone explain the output of bamstat5. it seems quite simple but i want to confirm description of output. i do not understand here whats the exactly meaning of mincov, maxcov and avg ??? Here is the output: #chrom start end ...
genome next-gen bamstats05 sequence alignment written 12 days ago by DL10 • updated 12 days ago by Pierre Lindenbaum109k
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Regarding Cnvkit analysis
... Hello, I am new to use cnvkit and i read manual of cnvkit. I did not understand so many things. I want to used cnvkit to calculate copy number in my sequencing data with no normal sample. So i followed the steps that mentioned in manual. In my analysis, i have target file that include all the exon ...
cnvkit written 5 months ago by DL10 • updated 5 months ago by Eric T.2.2k
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Regarding GC correction in sequencing data
... Hello, I have gone through some papers but i can not get that why GC content estimation and correction is important for CNV analysis ?? Can anyone explain me ?? Thanks & Regards ...
genome R next-gen sequencing written 6 months ago by DL10 • updated 6 months ago by Rob2.4k
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Regarding cnvrd2 package
... Hello, Can anyone tell that cnvrd2 package is specific for human genome or can i implement other genome also in it ?? Thanks in advance ...
R next-gen sequencing written 6 months ago by DL10
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Comment: C: Regarding sliding window for CNV analysis
... Thank you so much for useful advice. I am going through cnvkit tool but i am confused because i do not have experiment and control sample. In cnvkit, they used normal and tumor samples but i have 3 WGS data and reference sequence then how can i utilized cnvkit. Please suggest me. ...
written 6 months ago by DL10
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Comment: C: Regarding sliding window for CNV analysis
... Thank you so much for your reply.Ok, i will look upon cnvkit and FACETS. Can you just tell me that i count the reads in given window but i do not know i am right or wrong: 1. i divide the genome using makewindows command in 10kb. 2.bam2bed < DC_mapped.bam | awk '{if($5>35)print $0}' | bedmap ...
written 7 months ago by DL10

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Popular Question 12 days ago, created a question with more than 1,000 views. For Regarding Split reads and discordant reads

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