If you use the sort command suggested by cufflinks
Something like this (it should be printed out when it gives the sorting error):
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
Then it will work
the (-k 3,3) indicates that the reference contig name must also be sorted.
-
cufflinks version 0.8.2 vs 0.8.3
I ran 0.8.2 few months ago for a project and it worked fine on my .SAM files. After downloading 0.8.3, it started giving me a sort error.
I sorted my files exactly the same way as I did with 0.8.2. My .SAM file actually works with 0.8.2, but not 0.8.3. Is there something new with how it checks sorting in the new version? I noticed it was throwing me a sorting error based on reference contig name. Do I need to sort my .SAM file based on reference contig name and coordinates in the new version?
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
Leave a comment: