User: rsafavi

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rsafavi40
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r******@ucsc.edu

Posts by rsafavi

<prev • 19 results • page 1 of 2 • next >
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HUGO and Ensembl ids
... if we have "genes with the same HUGO ids but different Ensembl id" does it make sense to add up the raw count of those? ( for RNA expression or single cell analysis). Does it make sense to treat them as isoforms? ...
ensembl hugo rna-seq single cell written 7 weeks ago by rsafavi40 • updated 4 weeks ago by EagleEye6.0k
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Comment: C: Why am I getting different ensembl gene ids for a given gene symbol?
... if we have "genes with the same hogu ids but different ensemble id" does it make sense to add up the raw count of those? ( for RNA expression or single cell analysis). Does it make sense to treat them as isoforms? ...
written 8 weeks ago by rsafavi40
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Comment: C: Remove secondary alignments in RNA-seq analysis?
... What if you want to assemble the transcript? Do you still suggest to keep or remove the secondary alignments and the supplementary? ...
written 4 months ago by rsafavi40
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Answer: A: Get all the nucleotides from a bam file that is aligning to specific position in
... I figured it out. I had to put -Q 0 ( base quality) for Nanopore data ...
written 4 months ago by rsafavi40
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Comment: C: Get all the nucleotides from a bam file that is aligning to specific position in
... I am working with Nanopore cDNA data. I tried samtool mpileup before like this: samtools mpileup intersectedReads.bam -r chr1:13625035-13625035 > intersectedReads.pileup as a test case, but I got: chr1 13625035 N 0 * * chr1 13625036 N 0 * ...
written 4 months ago by rsafavi40
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Get all the nucleotides from a bam file that is aligning to specific position in the genome
... Hello, I have an alignment bam file, and I would like to retrieve all the bases aligning to that specific location in the genome. For example, if I am interested in position X in the genome, I would like to extract all the nucleotides that are aligning to that position X from my alignment file ...
genome samtools alignment position pysam written 4 months ago by rsafavi40
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Comment: C: Finding intergenic regions in bed file?
... Does this take care of overlapping genes? ...
written 5 months ago by rsafavi40
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Comment: C: featureCounts for aligned reads
... One more question, is having this warning normal? I get it with -p option WARNING: reads from the same pair were found not adjacent to each || || other in the input (due to read sorting by location or || || reporting of multi-mapping read pairs). ...
written 5 months ago by rsafavi40
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Comment: C: featureCounts for aligned reads
... Works perfectly thank you very much! ...
written 5 months ago by rsafavi40
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featureCounts for aligned reads
... Hi everyone, I have paired-end RNAseq data, and I used STAR aligner to do alignment, so basically for each paired-end fastq files I ended-up creating one alignment file (bam). Now I would like to create a count matrix to do DE analysis. I would like to use featureCounts tool. I was wondering what a ...
rnaseq differential featurecounts de expression written 5 months ago by rsafavi40 • updated 5 months ago by genomax59k

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