User: mah19

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mah190
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Posts by mah19

<prev • 7 results • page 1 of 1 • next >
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Comment: C: RNA-seq Differential expression analysis show no differentially expressed genes
... Thank you for your feedback. It helps confirm our interpretation of what we have seen so far. ...
written 28 days ago by mah190
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Comment: A: RNA-seq Differential expression analysis show no differentially expressed genes
... Sorry, I was trying to figure out how to upload a picture. The lnc RNA had been verified in previous literature as a modifier of several downstream genes. we have verified the effect of knockdown of this lncRNA on one of these genes via QPCR prior to going to RNA-seq. So we still believe that the bi ...
written 28 days ago by mah190 • updated 28 days ago by ATpoint26k
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RNA-seq Differential expression analysis show no differentially expressed genes with DEseq2
... Hello, We are investigating the knockdown effect of a specific long non-coding RNA lncRNA in cancer cell lines in an attempt to identify downstream target genes of this lncRNA. After knock-down(KD) we performed RNA-seq on KD vs wild type (WT) cells , and followed standard bioinformatics pipeline f ...
deseq2 lowly_expressed_genes rna-seq written 28 days ago by mah190 • updated 26 days ago by Charles Warden7.5k
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Comment: C: Detecting highly variable genes within replicates
... Hello Michele, If I understand your approach correctly, you are calculating the total variance on assumption that the data points( normalized read counts for a certain gene across replicates) follow a normal distribution and then calculating the shot noise on assumption that the same data points fo ...
written 9 months ago by mah190
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Run Defuse gene fusion detection software with mm10 RNA-Seq
... Hello, I am trying to run defuse to detect gene fusion in mouse RNA-Seq data. Anyone has an idea of how to adjust the config.txt file to run with the proper mus_musculus references? The defuse_run.pl file as well seems to be hard coded to get Homo-sapiens reference files from Ensembl website. Thank ...
defuse rna-seq gene_fusion written 20 months ago by mah190
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Comment: C: Visualizing Transcriptional Structural variants in bedpe format
... Hello Hussain, Thank you for your reply. Unless I m doing something wrong IGV will only show you one section of the variant at as it aligns to its location on the genome. I am interested to see how TSVs connect different genomic regions together in a graphical manner. Thanks ...
written 2.0 years ago by mah190
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Visualizing Transcriptional Structural variants in bedpe format
... Hello, I have generated transcription structural variant files from RNA-Seq data in Bedpe format by running chimeric Bam files with SQUID. Is there a way to visualize these files and locate the variants on their relevant positions on the reference genome, ie some tool that can show the variants a ...
tsv written 2.1 years ago by mah190 • updated 2.1 years ago by Hussain Ather940

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