Identify new transcripts using non-sorted bam file?

Question

[Cacau]

I would like to identify new transcripts with unsorted bam file. I know that cufflinks only works for sorted one. Which software should I use?

[John]

Why cant you just sort the BAM? :) Matching reads without a sort is going to take MUCH longer than matching reads with a sort.

[Rohit]

Any reason why you would not like to sort the file... just curious as sorting would be the first thing you would do with most downstream analyses tools

Answer 1

[mastal511]

Use samtools sort then samtools index to sort the bam file.