User: Varun Gupta

gravatar for Varun Gupta
Varun Gupta1000
Reputation:
1,000
Status:
Trusted
Location:
United States
Last seen:
3 days, 11 hours ago
Joined:
6 years, 9 months ago
Email:
g************@gmail.com

Posts by Varun Gupta

<prev • 217 results • page 1 of 22 • next >
0
votes
0
answers
175
views
0
answers
Comment: C: Picard Mark Duplicates
... Does picard takes soft clipped bases into account then? ...
written 5 weeks ago by Varun Gupta1000
0
votes
0
answers
175
views
0
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 5 weeks ago by Varun Gupta1000
0
votes
0
answers
175
views
0
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 5 weeks ago by Varun Gupta1000
2
votes
0
answers
175
views
0
answers
Picard Mark Duplicates
... 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 ...
picard markduplicates written 5 weeks ago by Varun Gupta1000
1
vote
1
answer
173
views
1
answers
Comment: C: genomeCoverageBed for per nucleotide coverage
... 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 7 weeks ago by Varun Gupta1000
0
votes
1
answer
173
views
1
answers
Comment: C: genomeCoverageBed for per nucleotide coverage
... 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 7 weeks ago by Varun Gupta1000
5
votes
1
answer
173
views
5 follow
1
answer
genomeCoverageBed for per nucleotide coverage
... 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 ...
bedtools written 7 weeks ago by Varun Gupta1000 • updated 7 weeks ago by Kevin Blighe19k
0
votes
4
answers
362
views
4
answers
Comment: C: Saving IGV images for bigwig files
... ![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 3 months ago by Varun Gupta1000
0
votes
4
answers
362
views
4
answers
Comment: C: Saving IGV images for bigwig files
... It got installed here /home/varun/.local/bin ...
written 3 months ago by Varun Gupta1000
0
votes
4
answers
362
views
4
answers
Comment: C: Saving IGV images for bigwig files
... pip install pyGenomeTracks ...
written 3 months ago by Varun Gupta1000

Latest awards to Varun Gupta

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Student 11 weeks ago, asked a question with at least 3 up-votes. For Read Counts In Intronic Region
Student 3 months ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
Popular Question 3 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Popular Question 5 months ago, created a question with more than 1,000 views. For RNA Seq datasets for different tissues not Poly-A selected
Great Question 5 months ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File
Teacher 5 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 8 months ago, created a question with more than 1,000 views. For RNA Seq datasets for different tissues not Poly-A selected
Teacher 8 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 8 months ago, created a question with more than 1,000 views. For Yeast genome SK1 strain
Student 8 months ago, asked a question with at least 3 up-votes. For Pombe Intron Locations
Great Question 8 months ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File
Popular Question 9 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 10 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Appreciated 10 months ago, created a post with more than 5 votes. For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For Bwa Mem -M Option
Guru 10 months ago, received more than 100 upvotes.
Popular Question 11 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 12 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 14 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 14 months ago, created a question with more than 1,000 views. For Tophat Junctions Bed File Strand Column
Great Question 14 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Epic Question 14 months ago, created a question with more than 10,000 views. For Bwa Mem -M Option
Student 14 months ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
Popular Question 15 months ago, created a question with more than 1,000 views. For Tophat Junctions Bed File Strand Column

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 938 users visited in the last hour