merging bam files
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6 months ago

For prediction of lncRNA, I have 6 bam files from different group of the experiment. I need to do assembly using StringTie software. Should I merge file first, or I can do it one by one. And what is the advantages of merging them. I tried to merge them but it give me error that bam file does not have valid header.

bam assembly lncRNA • 341 views
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The header of the BAM file contains information on the reference that was used and mapping parameters. You definitively must be sure that they were created with the same aligner using the identical reference to merge.

By merging, you increase the coverage. This will allow StringTie to call even very lowly expressed transcripts and possibly to determine the full length of transcripts more accurately. The downside of this approach is, that you will end up with fake transcripts studded together from fragments of different samples. Subsequently, you therefore need to scrutinize your initial transcripts by quantifying them in the single samples.

If merging is advisable depends on the sequencing depth of your single samples.


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