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 2.3 years 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 2.3 years 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 2.3 years ago by Varun Gupta1.1k • updated 2.3 years ago by dariober11k
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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 2.3 years 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 2.4 years 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 2.8 years 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 2.8 years 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 2.8 years 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 2.8 years 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 2.8 years ago by Varun Gupta1.1k • updated 2.8 years ago by genomax83k

Latest awards to Varun Gupta

Great Question 4 months ago, created a question with more than 5,000 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
Popular Question 7 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
Student 10 months ago, asked a question with at least 3 up-votes. For Has Any One Used Cummerbund
Epic Question 10 months ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Popular Question 12 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 12 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 12 months ago, created a question with more than 10,000 views. For Wiggle File 2 Bed File
Epic Question 12 months ago, created a question with more than 10,000 views. For Bwa Mem -M Option
Great Question 16 months ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Popular Question 17 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 17 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: What Is A "Spot" In Sra Format
Great Question 18 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Appreciated 18 months ago, created a post with more than 5 votes. For A: What Is A "Spot" In Sra Format
Great Question 20 months ago, created a question with more than 5,000 views. For Genotype Likelihoods
Popular Question 22 months ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Great Question 2.0 years ago, created a question with more than 5,000 views. For Mismatch Option In Bowtie2
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Removing low quality ends from a fastq file
Student 2.2 years ago, asked a question with at least 3 up-votes. For Read Counts In Intronic Region
Student 2.3 years ago, asked a question with at least 3 up-votes. For Homologous Genes In Mouse For Given Human Genes
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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