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alexstaj / cutadapt

Automatically exported from code.google.com/p/cutadapt
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bam format and stdin/stdout #31

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?

Please provide any additional information below.

Would you consider adding support for bam format as an input and output, or/and 
stdin/stdout to pipe it to other scripts? That would be fantastic!!

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

Thanks for your great software.

Carlos

Original issue reported on code.google.com by ctorr...@googlemail.com on 25 Oct 2011 at 2:35

GoogleCodeExporter commented 9 years ago 
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.

Original comment by marcel.m...@tu-dortmund.de on 26 Oct 2011 at 9:00

GoogleCodeExporter commented 9 years ago 
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"

Original comment by jwad...@gmail.com on 8 May 2012 at 9:23

GoogleCodeExporter commented 9 years ago 
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.

Original comment by marcel.m...@tu-dortmund.de on 8 Oct 2014 at 8:08

GoogleCodeExporter commented 9 years ago

Original comment by marcel.m...@tu-dortmund.de on 16 Oct 2014 at 8:26