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estepi / ASpli

Analysis of alternative splicing using RNAseq
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All NAs using ASpli for all splicing events #20

Closed OnkarMulay closed 2 years ago

OnkarMulay commented 2 years ago

I had run ASpli for 24 samples 12 and 22 in each group. I got reports for : asd <- jCounts(counts=gbcounts, features=features, minReadLength=200) --> all NAs

Code:

library("ASpli") library("GenomicFeatures") library("statmod")

GTF Preprocessing -----

gtfFileName <- "/scratch/zq45/om4416/HomoSapiens/Homo_sapiens.GRCh38.100.chr.gtf" genomeTxDb <- makeTxDbFromGFF(gtfFileName)

Feature Extraction ----

features <- binGenome( genomeTxDb )

Bam and Traget ------

BAMFiles <- c("bam1_1/Aligned.sortedByCoord.out.bam","bam1_2/Aligned.sortedByCoord.out.bam", "bam1_3/Aligned.sortedByCoord.out.bam","bam1_4/Aligned.sortedByCoord.out.bam", "bam1_5/Aligned.sortedByCoord.out.bam","bam1_6/Aligned.sortedByCoord.out.bam", "bam1_7/Aligned.sortedByCoord.out.bam","bam1_8/Aligned.sortedByCoord.out.bam", "bam1_9/Aligned.sortedByCoord.out.bam","bam1_10/Aligned.sortedByCoord.out.bam", "bam1_11/Aligned.sortedByCoord.out.bam","bam1_12/Aligned.sortedByCoord.out.bam", "bam2_2/Aligned.sortedByCoord.out.bam","bam2_3/Aligned.sortedByCoord.out.bam", "bam2_4/Aligned.sortedByCoord.out.bam","bam2_5/Aligned.sortedByCoord.out.bam", "bam2_6/Aligned.sortedByCoord.out.bam","bam2_7/Aligned.sortedByCoord.out.bam", "bam2_8/Aligned.sortedByCoord.out.bam","bam2_9/Aligned.sortedByCoord.out.bam", "bam2_10/Aligned.sortedByCoord.out.bam","bam2_11/Aligned.sortedByCoord.out.bam", "bam2_12/Aligned.sortedByCoord.out.bam","bam2_13/Aligned.sortedByCoord.out.bam",

targets <- data.frame(row.names = paste0('Sample_',c(1:24)),bam = BAMFiles[1:24],f1 = rep(c("O","B"),times=c(12,12)),stringsAsFactors = FALSE)

Counting against Annotated Features ----

gbcounts <- gbCounts(features=features, targets=targets, libType="PE", minReadLength = 200, maxISize = 50000)

Junction Based Denovo and splicing estimation ----

asd <- jCounts(counts=gbcounts, features=features, libType="PE", minReadLength=200) Is the code correct?

Why do I get all NAs ? No event is found

binGenome(TxDb) output:

estepi commented 2 years ago

Hi Onkar,

Can you open this issue here? https://github.com/chernolab/ASpli/issues

I see you have: 24 samples 12 and 22 in each group If you have your gbcounts object already done, we can inspect it and see how is the coverage in general you have

Maybe it is a good idea to split data by chunks... or to merge replicates to have a first idea

Which is your question here? Compare one group against the other?

We did run 50 control vs 50 treat and ASpli did well

thanks in advance

OnkarMulay commented 2 years ago

Ok, sure I'll open there and post the gbcounts there only. No, my question is what has happened that I get NA everywhere in : asd <- jCounts(counts=gbcounts, features=features, libType="PE", minReadLength=200)

Thank you