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8.4 years ago
Rashedul Islam ▴ 450
I got RNA-seq bam files that are aligned by BWA. When I am using these bam files in cuflinks I got following errors.
"BAM record error: found spliced alignment without XS attribute"
My command was:
./cufflinks -p 24 -G /path/Homo_sapiens.GRCh37.69.gtf -o /path/Cufflink_Out/ /path/test.bam
Can anyone help me?
Thanks a lot Manu. I did not map the reads to the reference genome and got the bam files from other source. So, I do not know whether the data is stranded or not. Right now it is not possible for me to remap with TopHat or STAR. However, I tried with specifying 3 different library types to run cufflinks e.g., fr-unstranded, fr-firststrand and fr-secondstrand. Only fr-secondstrand gave me the FPKM values of gene, isoforms and transcripts. fr-unstranded gave error
BAM record error: found spliced alignment without XS attributeand fr-firststrand was aborted and the last line was
7ffcbb0b3000-7ffcbb0b4000 rw-p 00000000 00:00 0 Aborted.
So, can I rely on the FPKM values of fr-secondstrand library type? Please let me know. Thanks in advance.
I am not sure about it. But I think Istvan Albert, Pierre Lindenbaum or Devon Ryan could probably answer this
If possible get fastq files from source and then map with tophat or STAR
I am getting this similar thing.Is this an error because I have got my output files generated?
Also I have used STAR as my aligner and still getting this issue.Let me know your thoughts.
I solved the error by adding the library type in Cufflinks. My command was:
DId you find the change in results?I saw that output files are still generated in the case where it shows an error.
I did not get any error finally.