User: novicebioinforesearcher

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Posts by novicebioinforesearcher

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Obtain reads mapping to splice junctions
... will this work just did a bit or more research > To generate read counts, you must run QoRTs [4] on each aligned bam > file. QoRTs includes a basic function that calculates a variety of QC > metrics along with gene-level and splice-junction-level counts. All > these functions can be pe ...
written 11 weeks ago by novicebioinforesearcher40
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Comment: C: Obtain reads mapping to splice junctions
... So is there any way to do this outside of using those splicing tools? we have curated list of splice junctions that have been seen to change in certain conditions, (around 200 junctions), we did match those 200 with hisat2's script output and now just need reads mapping to it will bedtools perform s ...
written 11 weeks ago by novicebioinforesearcher40
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Obtain reads mapping to splice junctions
... we have RNA seq bam aligned using Hisat2, since hisat provides `hisat2_extract_splice_sites.py` script which gives co ordinates for splice junctions was wondering if some one could point us to how we can obtain reads mapping to these junctions something similar to Htseq where it provides genes mapp ...
splicing rna-seq written 11 weeks ago by novicebioinforesearcher40
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Comment: C: Alternative Splicing Annotation of Exons and Introns
... how did u get the code? ...
written 8 months ago by novicebioinforesearcher40
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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 11 months ago by novicebioinforesearcher40
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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 12 months ago by novicebioinforesearcher40
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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 12 months ago by novicebioinforesearcher40
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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 12 months ago by novicebioinforesearcher40
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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 12 months ago by novicebioinforesearcher40 • updated 12 months ago by Brian Bushnell15k
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Comment: C: Miseq Genomic DNA analysis
... we are working on mouse ...
written 12 months ago by novicebioinforesearcher40

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Rising Star 12 months ago, created 50 posts within first three months of joining.
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