I used Hisat2 output sam file directly in cufflinks and getting error: Please suggest what to do?
[root@psgl hisat2]# /home/yog/software/cufflinks-2.2.1.Linux_x86_64/cufflinks -g gene.gtf -p 8 -o
/data/SNU_work/Analysis/unmapped/unmapped/hisat2/assembly/ --no-update-check unmap.sam
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File unmap.sam doesn't appear to be a valid BAM file, trying SAM...
[06:07:50] Loading reference annotation.
[06:07:51] Inspecting reads and determining fragment length distribution.
Processing Locus R8:5812456-5812792 [ ] 0%
Error: this SAM file doesn't appear to be correctly sorted!
current hit is at R3:14022855, last one was at R8:5822720
Cufflinks requires that if your file has SQ records in
the SAM header that they appear in the same order as the chromosomes names
in the alignments.
If there are no SQ records in the header, or if the header is missing,
the alignments must be sorted lexicographically by chromsome
name and by position.