User: Varun Gupta

gravatar for Varun Gupta
Varun Gupta900
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900
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3 months ago
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6 years, 3 months ago
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Posts by Varun Gupta

<prev • 203 results • page 1 of 21 • next >
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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 3 months ago by Varun Gupta900
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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 3 months ago by Varun Gupta900
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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 3 months ago by Varun Gupta900
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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 3 months ago by Varun Gupta900
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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 3 months ago by Varun Gupta900 • updated 3 months ago by genomax39k
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Comment: C: Any tools to quantify intron retention in RNAseq data?
... Hi Devon, I am trying to run your script on seqanswer. With hg19.gff(generated from DEXSeq python scripts), I am using import.gff2 as per your command but 1. It does not use `asRangedData=F` 2. Also it gives warnings as closing unused connection 4 (Homo_changed_37.74.gff) after I remove `asRangeDa ...
written 4 months ago by Varun Gupta900
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Comment: C: exon quantification for tissue samples
... Hi, I thought of inserting the exon in the GTF file. I will insert it and see what I get for my exon. I should use featureCounts since I have a bed file for the exon already. I will give it a try and let you know Thanks ...
written 9 months ago by Varun Gupta900
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exon quantification for tissue samples
... Hi Everyone, I have some tissue RNA-SEQ samples and I have mapped it to hg19 ref genome to get the bam files. I am trying to get the exon counts for a particular exon for all those tissue samples from the bam files. This exon is not annotated in the gif/gff file. I have the coordinates of this exon ...
count exon rna-seq splice written 9 months ago by Varun Gupta900 • updated 9 months ago by EagleEye4.8k
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genomeCoverageBed : for fixed size bins
... Hi Everyone, I am trying to go from a bam file to a bedgraph file where I have fixed intervals of 100bp. chr1 0 100 4 chr1 100 200 5 chr1 200 300 6 ... I have used genomeCoverageBed to compute the coverage, but can I use it to output counts in fixed window sizes of 100bp?? I would ...
bedtools written 11 months ago by Varun Gupta900 • updated 11 months ago by apa@stowers320
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Comment: C: cutadapt for trimming reads to specific length
... I was using cutadapt so thought this would be possible using it. I will look into fastq_trimmer. Thanks ...
written 13 months ago by Varun Gupta900

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