User: snishtala03

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Posts by snishtala03

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Comment: C: SAM flag and select reads that map uniquely
... Hi Devon, great discussion. I merged R1 and R2 and then aligned them to the reference. Now, I see that some of my reads have flag 16 and some have 0. Just trying to understand what is happening here in my case. ...
written 4 hours ago by snishtala030
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Comment: C: Get read start site using bedtools from bam file after merging paired end data
... Also, Here is an example of stats when I use bbmerge - Pairs: 1071898 Joined: 1003105 93.582% Ambiguous: 63915 5.963% No Solution: 4878 0.455% Too Short: 0 0.000% Avg Insert: 165 ...
written 5 hours ago by snishtala030
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Comment: C: Get read start site using bedtools from bam file after merging paired end data
... My read length is around 150 bps, so it is > 0.5*insert length. I did map the reads as paired end directly to the reference. But my reference is circular. So, I was suggested to merge the reads to see how the alignments look. ...
written 5 hours ago by snishtala030
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Get read start site using bedtools from bam file after merging paired end data
... Hello, I have some paired end viral RNA-Seq data. For some analysis requested by my collaborator, I am trying to do the analysis by merging R1 and R2. So this is my analysis so far - 1. I merge read1.fq and read2.fq using bbmerge. 2. Then, use bwa mem to align reads to the reference viral gen ...
bbmerge bedtools alignment samtools rna-seq written 1 day ago by snishtala030
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read simulation and quantification
... Hello, I have fasta sequences of 7 viral RNA transcripts. I need to see if I can recover the correct counts of these transcripts. I am guessing I will first have to use a software ( like polyester or rsem) to generate simulated fastq files for these transcripts and then use a transcript assemble ...
fasta simulation quantification rna-seq written 18 months ago by snishtala030
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Comment: C: GAGE or GSEABase using expression data and pathway.gmt file for mouse
... I need to do gene set enrichment for multiple (20) data sets. I was looking for a R option, so I can automate it and it would be faster. ...
written 22 months ago by snishtala030
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
... Hello, I have mouse data for 8 samples (2 conditions, 4 samples each). I performed RNA-Seq analysis and have expression data for different genes across these 8 samples. I also downloaded pathway file from http://download.baderlab.org/EM_Genesets/April_01_2017/Mouse/symbol/Mouse_AllPathways_April_01 ...
pathway R rna-seq gsea gage written 22 months ago by snishtala030 • updated 22 months ago by bigmawen310
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Comment: C: How to convert UCSC transcript(isforms) ids to Ensemble transcript ids?
... I have a similar problem. I downloaded level 3 isoform level data from TCGa and they have UCSC IDs there. I tried Biomart, DAVID, and also some other conversion tools online. The problem is most of the IDs do not match to any Ensembl ID. I tried to look the other way round online too (i.e my transcr ...
written 2.1 years ago by snishtala030

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Popular Question 17 months ago, created a question with more than 1,000 views. For GAGE or GSEABase using expression data and pathway.gmt file for mouse

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