User: Varun Gupta
Varun Gupta • 1.1k
- Reputation:
- 1,130
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 2 days, 3 hours ago
- Joined:
- 8 years, 1 month ago
- Email:
- g************@gmail.com
Posts by Varun Gupta
<prev
• 218 results •
page 1 of 22 •
next >
1
vote
1
answer
1.1k
views
1
answer
... Hi,
I want to filter my fastq reads based on ambiguous characters, basically **N's**. So if I have a read sequence having N's greater than 5%, I want to discard that read, if lower than 5%, I want to keep it. It would be really helpful if someone know about any tool which already does that.
Thanks ...
written 16 months ago by
Varun Gupta • 1.1k
• updated
16 months ago by
Pierre Lindenbaum ♦ 123k
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: Picard Mark Duplicates
... Does picard takes soft clipped bases into account then? ...
written 18 months ago by
Varun Gupta • 1.1k
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: Picard Mark Duplicates
... Hi finswimmer,
I tried the same thing with samtools rmdup and it considers them as duplicates and retains the one with high mapping quality. Regarding the soft clip bases, I don't think soft clipped bases has to do with this thing because the position 88015806 in the above example is the position st ...
written 18 months ago by
Varun Gupta • 1.1k
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: Picard Mark Duplicates
... Thanks Pierre. Can we provide a list of Barcodes and not 1 BARCODE sequence to BARCODE_TAG option? The library was indeed created with Unique Molecular Barcodes(96 of them) ...
written 18 months ago by
Varun Gupta • 1.1k
2
votes
1
answer
2.0k
views
1
answer
... Hi,
I have used Picard MarkDuplicates tool to remove duplicates from my bam file. Understanding it correctly, if there are more than 1 reads starting at the same position, then after removing for duplicates, only 1 read will be present in the bam file generated from MARKDUPLICATES based on its qual ...
written 18 months ago by
Varun Gupta • 1.1k
• updated
16 months ago by
marcela.uliano • 60
1
vote
1
answer
910
views
1
answers
... yup, works fine, must say better than genomeCoverageBed because in genomeCoverageBed, if you have all the headers(having all the chromosomes) in the bam file and only a particular chr alignments you want, it still goes through all the chromosomes.
...
written 18 months ago by
Varun Gupta • 1.1k
0
votes
1
answer
910
views
1
answers
... Hi Kevin,
Thanks for your reply. I looked at the bedtools manual for coverage function. If I want per nucleotide coverage for the bed file(as is my case), the command should be like this
bedtools coverage -a mygenes.bed -b test.bam -d
Then this is the output
chr5 10000 23456 10001 14
...
written 18 months ago by
Varun Gupta • 1.1k
6
votes
1
answer
910
views
6 follow
1
answer
... Hello,
I want to get per nucleotide coverage for my particular gene (geneX) which I added in the fasta file. There are other chromosomes present in the bam file, whose per nu coverage I am not interested in. When I use genomeCoverageBed tool to calculate per nucleotide coverage for my gene I also g ...
written 18 months ago by
Varun Gupta • 1.1k
• updated
18 months ago by
Kevin Blighe ♦ 49k
0
votes
4
answers
1.1k
views
4
answers
... ![enter image description here][1]Hi Venu,
I tried making plots by providing this command
./pyGenomeTracks --tracks tracks.ini --BED ~/test.bed -out fig_
The graph is showing too much upstream and downstream of my bed coordinates. Any way to fix that
Also how can i display the name of the feat ...
written 20 months ago by
Varun Gupta • 1.1k
0
votes
4
answers
1.1k
views
4
answers
... It got installed here
/home/varun/.local/bin ...
written 20 months ago by
Varun Gupta • 1.1k
Latest awards to Varun Gupta
Popular Question
5 days ago,
created a question with more than 1,000 views.
For extracting matched part(M) only for the sequence from the CIGAR string
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For extracting matched part(M) only for the sequence from the CIGAR string
Epic Question
3 months ago,
created a question with more than 10,000 views.
For Wiggle File 2 Bed File
Popular Question
4 months ago,
created a question with more than 1,000 views.
For extracting matched part(M) only for the sequence from the CIGAR string
Popular Question
5 months ago,
created a question with more than 1,000 views.
For extracting matched part(M) only for the sequence from the CIGAR string
Epic Question
5 months ago,
created a question with more than 10,000 views.
For Wiggle File 2 Bed File
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: What Is A "Spot" In Sra Format
Great Question
8 months ago,
created a question with more than 5,000 views.
For Mismatch Option In Bowtie2
Popular Question
9 months ago,
created a question with more than 1,000 views.
For extracting matched part(M) only for the sequence from the CIGAR string
Popular Question
10 months ago,
created a question with more than 1,000 views.
For Removing low quality ends from a fastq file
Good Answer
11 months ago,
created an answer that was upvoted at least 5 times.
For A: What Is A "Spot" In Sra Format
Great Question
11 months ago,
created a question with more than 5,000 views.
For Genotype Likelihoods
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: What Is A "Spot" In Sra Format
Great Question
13 months ago,
created a question with more than 5,000 views.
For Genotype Likelihoods
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Removing low quality ends from a fastq file
Great Question
17 months ago,
created a question with more than 5,000 views.
For Mismatch Option In Bowtie2
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Removing low quality ends from a fastq file
Student
19 months ago,
asked a question with at least 3 up-votes.
For Read Counts In Intronic Region
Student
20 months ago,
asked a question with at least 3 up-votes.
For Homologous Genes In Mouse For Given Human Genes
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Removing low quality ends from a fastq file
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
Popular Question
22 months ago,
created a question with more than 1,000 views.
For RNA Seq datasets for different tissues not Poly-A selected
Great Question
22 months ago,
created a question with more than 5,000 views.
For Tophat Junctions.Bed File
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1702 users visited in the last hour