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Forum: Bioinformatics 08-06-2019, 12:07 AM
Replies: 240
Views: 88,532
Posted By bartn
another program that is often used for these...

another program that is often used for these cases is DIAMOND

https://github.com/bbuchfink/diamond

But like GenoMax said you have to do some post processing of the output to get to the format...
Forum: Bioinformatics 07-10-2019, 06:09 AM
Replies: 240
Views: 88,532
Posted By bartn
That's indeed unfortunate. I might try sending an...

That's indeed unfortunate. I might try sending an email. A previous bug report was solved very quickly!

One of the reasons I like about BBMap is indeed the wide range of statistics it can...
Forum: Bioinformatics 07-10-2019, 12:13 AM
Replies: 240
Views: 88,532
Posted By bartn
From the description of the option I understood...

From the description of the option I understood it can be used for RNA as well:

metagenome=f Assign scaffolds a random exponential coverage level, to simulate a metagenomic or RNA coverage...
Forum: Bioinformatics 07-09-2019, 08:31 AM
Replies: 240
Views: 88,532
Posted By bartn
Yes, that does seem to increase the mapping...

Yes, that does seem to increase the mapping percentages. Any idea why it is not working with meta option? Changes read length and insert size does not seem to do much..
The plasmid is about 0.5MB...
Forum: Bioinformatics 07-09-2019, 12:02 AM
Replies: 240
Views: 88,532
Posted By bartn
randomreads.sh

Hi!

I want to created a (small) RNAseq test set from a small bacterial plasmid. So I used :
randomreads.sh reads=30000 paired=t metagenome=t ref=transcripts.fasta out1=test_RNA_1.fq...
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