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cufflinks large bundles warning

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
cufflinks star
• 2,379 views • link
written by Sam Sam

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?

• 1 views • link
written by Sam Sam

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

• 1 views • link
written by Bastien Hervé Bastien Hervé

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

• 1 views • link
written by Sam Sam

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

• 1 views • link
written by Bastien Hervé Bastien Hervé

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