Identify new transcripts using non-sorted bam file?
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?
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Use samtools sort then samtools index to sort the bam file.
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Why cant you just sort the BAM? :) Matching reads without a sort is going to take MUCH longer than matching reads with a sort.
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