Question: cufflinks large bundles warning
0
gravatar for Sam
11 months ago by
Sam120
Sam120 wrote:

Dear All

I used star to align the PE lib with this command and then I converted sam file to bam and sorted it with samtools but after running the cufflinks I got "Warning: Skipping large bundle" how I can fix it ?

Thanks

STAR --runThreadN 12 --genomeDir  /genome_index_star -sjdbGTFfile /genome_index/Egene_exons.gtf --readFilesIn R1.fastq,R2.fastq --outFileNamePrefix test  --outSAMstrandField intronMotif

cufflinks -o cufflink_out_gtf -g ./Egene_exons.gtf test_Aligned.out_sorted.bam
star cufflinks • 382 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Sam120

Try to increase the --max-bundle-length in cufflinks command, try 10000000

similar error

cufflinks options

ADD REPLYlink modified 11 months ago • written 11 months ago by Bastien Hervé4.4k

but I tried also(the same lib ) with Tophat2 and Hisat2 and cufflinks worked well without any warning and error. should I change any flag in the star to be compatible with cufflinks?

ADD REPLYlink written 11 months ago by Sam120
1

In STAR manual

In addition, it is recommended to remove the non-canonical junctions for Cufflinks runs using --outFilterIntronMotifs RemoveNoncanonical.

jM jI attributes require samtools 0.1.18 or later, and were reported to be incompatible with some downstream tools such as Cufflinks.

I would say also that what you got is just a warning not an error

ADD REPLYlink written 11 months ago by Bastien Hervé4.4k

Thanks for your help, but with this warning, the processing time of cufflinks increased at least 10 times.

ADD REPLYlink modified 11 months ago • written 11 months ago by Sam120

Did you try the --max-bundle-length and the --outFilterIntronMotifs RemoveNoncanonical ?

ADD REPLYlink written 11 months ago by Bastien Hervé4.4k
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