User: rsafavi

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rsafavi40
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5 months, 2 weeks ago
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r******@ucsc.edu

Posts by rsafavi

<prev • 17 results • page 1 of 2 • next >
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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 8 days 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 22 days 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 23 days 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 23 days ago by rsafavi40
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Comment: C: Finding intergenic regions in bed file?
... Does this take care of overlapping genes? ...
written 6 weeks 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 7 weeks ago by rsafavi40
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Comment: C: featureCounts for aligned reads
... Works perfectly thank you very much! ...
written 7 weeks 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 7 weeks ago by rsafavi40 • updated 7 weeks ago by genomax54k
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What is the difference between Repeat Masker and Window Masker from genom browser
... Would someone please explain the difference between window masker and repeat masker? ...
windowmasker genombrowser repeatmasker written 8 weeks ago by rsafavi40
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Answer: A: Filtering rRNA from RNAseq data
... RSeQC tool works with the bam file. It takes in an rRNA bed file and alignment file and it splits your reads into rRNA aligned reads, reads that did not align to rRNA, and qcfailed,unmapped reads. Still, at the level of fastq file, I think sortmerna is a good tool, but it requires rRNA fasta ...
written 8 weeks ago by rsafavi40

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