User: Varun Gupta

gravatar for Varun Gupta
Varun Gupta940
Reputation:
940
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Trusted
Location:
United States
Last seen:
3 days, 10 hours ago
Joined:
6 years, 5 months ago
Email:
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Posts by Varun Gupta

<prev • 210 results • page 1 of 21 • next >
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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 18 days ago by Varun Gupta940
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Comment: C: Saving IGV images for bigwig files
... It got installed here /home/varun/.local/bin ...
written 18 days ago by Varun Gupta940
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Comment: C: Saving IGV images for bigwig files
... pip install pyGenomeTracks ...
written 18 days ago by Varun Gupta940
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Comment: C: Saving IGV images for bigwig files
... Hi venu, I downloaded and installed the pyGenomeTracks but I cannot locate make_tracks_file command for making the config file. Where does this go. I am using linux machine ...
written 18 days ago by Varun Gupta940
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Saving IGV images for bigwig files
... Hi, I have 100 bigwig files and a bed file which has 80 features. I want to load all the bigwig files and bed annotation file in IGV and for each feature I want to output an image which has for each feature all the loaded 100 bigwig files. In total I should have 80 graphs(for 80 features). Also I w ...
bigwig igv written 18 days ago by Varun Gupta940 • updated 17 days ago by dariober8.6k
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Comment: C: How To Efficiently Parse A Huge Fastq File?
... This works pretty well although I will say use this: grep -f ids.txt -F -A 3 seq.fq | grep -v '^--$' > 10000.fq This is because sometimes qaulity line can start with 2 -- and that would screw the results. ...
written 4 weeks ago by Varun Gupta940
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Comment: C: Any tools to quantify intron retention in RNAseq data?
... Reads in the Bam file created should be mapped to the transcriptome or whole genome?? ...
written 5 weeks ago by Varun Gupta940
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Comment: C: querying blast database for rna seq reads
... This microbial blast index might give me some idea quickly. To use this microbial blast index, I should just use blastn with my fastq reads on this index? Thanks genomax for the help ...
written 6 months ago by Varun Gupta940
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Comment: C: querying blast database for rna seq reads
... I created a reference fasta file for all the bacterial species and combined them into one fasta file. Taking this fasta file as genome, I want to map my paired-end RNA-Seq reads to this fasta file to see how many reads are coming from which bacterial species. Since I combined all the bacterial speci ...
written 6 months ago by Varun Gupta940
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Comment: C: querying blast database for rna seq reads
... Do you think indexing and mapping with an aligner would be an option to look into, although I think the genome to be indexed is very large 25G?? ...
written 6 months ago by Varun Gupta940

Latest awards to Varun Gupta

Student 14 days ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
Popular Question 24 days ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
Great Question 8 weeks ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File
Popular Question 8 weeks ago, created a question with more than 1,000 views. For RNA Seq datasets for different tissues not Poly-A selected
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
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 5 months ago, created a question with more than 1,000 views. For Yeast genome SK1 strain
Great Question 5 months ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File
Student 5 months ago, asked a question with at least 3 up-votes. For Pombe Intron Locations
Popular Question 6 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 7 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Appreciated 7 months ago, created a post with more than 5 votes. For A: Help With Perl Script: Store Fasta Sequences Into A Hash.
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Bwa Mem -M Option
Guru 7 months ago, received more than 100 upvotes.
Popular Question 8 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
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 11 months ago, created a question with more than 1,000 views. For Homologous Genes In Mouse For Given Human Genes
Popular Question 11 months ago, created a question with more than 1,000 views. For Tophat Junctions Bed File Strand Column
Great Question 11 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Epic Question 11 months ago, created a question with more than 10,000 views. For Bwa Mem -M Option
Student 11 months ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
Popular Question 12 months ago, created a question with more than 1,000 views. For Tophat Junctions Bed File Strand Column
Great Question 12 months ago, created a question with more than 5,000 views. For Wiggle File 2 Bed File
Student 12 months ago, asked a question with at least 3 up-votes. For Has Any One Used Cummerbund

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