Question: Cufflinks takes too long time on my PC
gravatar for scheme4193
5 weeks ago by
scheme41930 wrote:

I'm now running expression analysis from RNA-Seq sequence data.

I want to calculate FPKM value and make heat map by using R and I've already finish QC & mapping. So, I used cufflinks to calculate, and wanted to continue to next analysis like cuffmerge and cuffdiff.

However, cufflinks don't run smoothly ( it proceeds only 10% in an hour ).

QC was run by FastQC and fastq_quality_trimmer, and mapping was run by Hisat2. Also, Hisat2's result was sam, so I used samtools to convert sam to bam.

・This is commands that I actually ran.

"cufflinks -p 2 [annotation's gtf file] [bam file] -o [output folder]"

・This is the outputs displayed on screen

BAM record error: found spliced alignment without XS attribute

Processing Locus 6:160042173-160042246 [* ] 31%BAM record error: found spliced alignment without XS attribute

This is my computer's environment

・MacBook Pro, mac OS Mojave

・memory 8GB : CPU 2.9GHz, Intel Core i7, 2 cores

・annotation's gtf file 102MB , mapping results bam file 3.7 GB

Does anyone know why cufflinks takes so much time or is it usual in situation like my PC ?

Are there any mistake points or bad combination in my procedure ?

If my command is wrong, please tell me which is wrong or how should I write ? Also, do you think cufflinks is running normally considering about the outputs displayed on screen.


rna-seq next-gen • 107 views
ADD COMMENTlink written 5 weeks ago by scheme41930

A pipeline with low computational requirements is Salmon-tximport-DESeq2

ADD REPLYlink written 5 weeks ago by ATpoint16k

Thank you so much ! I'll try it

ADD REPLYlink written 5 weeks ago by scheme41930
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