bam format and stdin/stdout about cutadapt HOT 4 CLOSED

From [email protected] on October 26, 2011 02:00:43

Hi, thanks for your suggestion. I think it's a great idea. But just to clarify: Is this about two distinct suggestions? One being BAM input and output, the other being reading any file format from standard input and writing to standard output? The latter is already possible, just use dash "-" as the input file name. I've added a sentence to the command-line help to make this clearer.

Labels: -Type-Defect Type-Enhancement

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From [email protected] on May 08, 2012 14:23:40

The original request also mentioned:

"Also I would add the option to provide a txt file with the adaptors and their names to add them to the reports."

I currently use an conf file as you mentioned in the documentation to give cutadapt a long list of adapters. However, it would be nice, as the mentioned, to be able to "name" those adapters.

something like:
-a GATCGGAAGAGCACACGTCTGA "Tru-seq Adapter 1"

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From [email protected] on October 08, 2014 13:08:30

Hi Carlos, since you just filed issue #82 , maybe you could also comment on your report regarding BAM input/output. I'm wondering if I should just close this. I like the idea of storing reads in BAM files instead of FASTQ files, but I don't know if people are actually doing it.

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From [email protected] on October 16, 2014 13:26:45

Status: WontFix

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