User: Varun Gupta

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Varun Gupta1.1k
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Posts by Varun Gupta

<prev • 218 results • page 2 of 22 • next >
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Comment: C: Saving IGV images for bigwig files
... pip install pyGenomeTracks ...
written 17 months ago by Varun Gupta1.1k
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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 17 months ago by Varun Gupta1.1k
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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 17 months ago by Varun Gupta1.1k • updated 17 months ago by dariober10k
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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 18 months ago by Varun Gupta1.1k
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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 18 months ago by Varun Gupta1.1k
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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 23 months ago by Varun Gupta1.1k
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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 23 months ago by Varun Gupta1.1k
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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 23 months ago by Varun Gupta1.1k
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Comment: C: querying blast database for rna seq reads
... Hi, for that I have index my combined genome which is around 25G and has 12690 contigs. Do you think aligner would be fine indexing it and then mapping it? ...
written 23 months ago by Varun Gupta1.1k
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querying blast database for rna seq reads
... Hi, I downloaded all the bacterial genomes from ncbi (`ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt`) I concatenated all the fasta files into one file and created a database using makeblastdb. I have reads in fastq file which I believe has been contaminated with bacteri ...
blast blastn rna-seq written 23 months ago by Varun Gupta1.1k • updated 23 months ago by genomax69k

Latest awards to Varun Gupta

Epic Question 8 days ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Popular Question 8 weeks 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 8 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 10 weeks ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Bwa Mem -M Option
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Great Question 5 months ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
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 7 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Great Question 8 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Appreciated 8 months ago, created a post with more than 5 votes. For A: What Is A "Spot" In Sra Format
Great Question 10 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Popular Question 11 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Great Question 14 months ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
Popular Question 16 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Student 16 months ago, asked a question with at least 3 up-votes. For Read Counts In Intronic Region
Student 17 months ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Teacher 19 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 19 months ago, created a question with more than 1,000 views. For RNA Seq datasets for different tissues not Poly-A selected
Great Question 19 months ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File
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
Popular Question 22 months ago, created a question with more than 1,000 views. For Yeast genome SK1 strain
Great Question 22 months ago, created a question with more than 5,000 views. For Tophat Junctions.Bed File

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