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hisat2-cufflinks: BAM record error: found spliced alignment without XS attribute

I got alignment by using hisat2 with reference genome, and sort the sam file to bam file. when I used cufflinks to assemble the transcriptome, it gave the error

BAM record error: found spliced alignment without XS attribute

and also it gave four result files,genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf and transcripts.gtf file.My command is as follows:

cufflinks -p 2 --library-type fr-unstranded -o ly1_assemble_out ly1_sort.bam

who can help me how to fix the error? and should I trust the results?

assembly
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updated by lakhujanivijay lakhujanivijay • written by whlei • whlei

Hi whlei

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

I think issues like are already discussed on biostars. Look at the right hand side pane of your post under "Similar Posts"

Thank you!

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written by lakhujanivijay lakhujanivijay

Hello whlei!

We believe that this post does not fit the main topic of this site.

Duplicate post

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by lakhujanivijay lakhujanivijay

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