User: novicebioinforesearcher

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Posts by novicebioinforesearcher

<prev • 59 results • page 1 of 6 • next >
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Comment: C: Alternative Splicing Annotation of Exons and Introns
... how did u get the code? ...
written 6 weeks ago by novicebioinforesearcher30
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how to find common splicing events from mats output across multiple samples
... I have compared 5 different conditions using rMATS, which outputs 5 different files for each alternative splicing event. I would like to first find a common junctions in skipped exon (Event) across all this 5 conditions(text files) and write the read count and other meta information in a new file, ...
splicing rna-seq written 4 months ago by novicebioinforesearcher30
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Comment: C: Please help me with adapter-trimming
... Sure, some additional info about the experiment attempting to detect indels from a panel of clones resulting from CRISPR targeted deletion. Regions around the target were PCR amplified to produce a roughly 150bp amplicon, which was then sequenced with as a PE250 run. ...
written 5 months ago by novicebioinforesearcher30
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Comment: C: Please help me with adapter-trimming
... Apologies for incomplete information,Yes these were PCR amplicons that were sequenced, I aligned the reads using bwa mem, we were trying to induce a deletion and check if worked by sequencing exon 6 of a particular gene. ...
written 5 months ago by novicebioinforesearcher30
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Comment: C: which one is adapter and which one is index
... Thanks, will look in to it where can i find adapter sequences? that have been highlighted in fastqc and what about the seond file that has which I am guessing to be index ...
written 5 months ago by novicebioinforesearcher30
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Please help me with adapter-trimming
... I received fastq files from core they said they have de multiplexed it but when i ran fastqc i can still see some adapters, attached is figure ![Adapter seq fastqc][1] My question along with fastq files with names like this _TAGTCTTG_S7_L001_R1_001.fastq.gz _TAGTCTTG_S7_L001_R2_001.fas ...
trimming dna written 5 months ago by novicebioinforesearcher30 • updated 5 months ago by Brian Bushnell15k
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Comment: C: Miseq Genomic DNA analysis
... we are working on mouse ...
written 5 months ago by novicebioinforesearcher30
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Comment: C: Miseq Genomic DNA analysis
... Thank you,I will ask my admin to install bbMap meanwhile can this also be done using bwa mem? ...
written 5 months ago by novicebioinforesearcher30
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Miseq Genomic DNA analysis
... We have sequenced genomic dna using miseq 2x250, and have received fastq files, i was wondering how to go about with respect to alignment of these reads and check for indels and snps is there a specific work flow? ...
alignment genomic dna written 5 months ago by novicebioinforesearcher30 • updated 5 months ago by Brian Bushnell15k
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which annotation to use and is it advisable to use bam to fastq
... I need to reanalyze certain dataset(rna seq paired end stranded, 100bp) that has been already analyzed using a very old pipeline using mm9 reference (for all downstream analysis) and the files have been stored as bam(after alignment) 1. While using alignment tools like star or hisat2, which annota ...
alignment rna-seq written 5 months ago by novicebioinforesearcher30 • updated 5 months ago by WouterDeCoster24k

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Rising Star 5 months ago, created 50 posts within first three months of joining.
Supporter 6 months ago, voted at least 25 times.

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