User: Varun Gupta

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Varun Gupta1.1k
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Posts by Varun Gupta

<prev • 218 results • page 1 of 22 • next >
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Filtering reads on the basis of percentage of ambiguous(N's) characters
... 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 ...
filter fastq rna-seq written 2.0 years ago by Varun Gupta1.1k • updated 2.0 years ago by Pierre Lindenbaum129k
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Comment: C: Picard Mark Duplicates
... Does picard takes soft clipped bases into account then? ...
written 2.2 years ago by Varun Gupta1.1k
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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 2.2 years ago by Varun Gupta1.1k
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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 2.2 years ago by Varun Gupta1.1k
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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 2.2 years ago by Varun Gupta1.1k • updated 2.1 years ago by marcela.uliano60
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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 2.3 years ago by Varun Gupta1.1k
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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 2.3 years ago by Varun Gupta1.1k
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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 2.3 years ago by Varun Gupta1.1k • updated 2.3 years ago by Kevin Blighe61k
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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 2.4 years ago by Varun Gupta1.1k
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Comment: C: Saving IGV images for bigwig files
... It got installed here /home/varun/.local/bin ...
written 2.4 years ago by Varun Gupta1.1k

Latest awards to Varun Gupta

Appreciated 3 months ago, created a post with more than 5 votes. For A: What Is A "Spot" In Sra Format
Popular Question 3 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Epic Question 3 months ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Great Question 6 months ago, created a question with more than 5,000 views. For Wiggle File 2 Bed File
Popular Question 6 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 6 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 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 11 months ago, created a question with more than 1,000 views. For extracting matched part(M) only for the sequence from the CIGAR string
Student 11 months ago, asked a question with at least 3 up-votes. For Has Any One Used Cummerbund
Epic Question 12 months ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Popular Question 13 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 13 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 14 months ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Epic Question 14 months ago, created a question with more than 10,000 views. For Bwa Mem -M Option
Great Question 17 months ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Popular Question 18 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 19 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Great Question 20 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Appreciated 20 months ago, created a post with more than 5 votes. For A: What Is A "Spot" In Sra Format
Great Question 22 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Popular Question 23 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Great Question 2.1 years ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file

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