User: roussine
roussine • 0
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Posts by roussine
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... Alex - thanx indeed for this advice ...
written 12 months ago by
roussine • 0
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... Dear all,
can anyone share if there is a command-line utility for UNIX that would convert bootstrap/confidence values in trees from fractions (0-1) to integers (1-100)? Keeping intact branch lengths and OTU names.
Thanks a lot in advance. ...
written 12 months ago by
roussine • 0
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... Yes, it quite merges, a good peak at about 170 bases (~ 4/5 of all 100 bases-reads merge).
Do I get right that you do not see any contras against using the merged portion for SE assemblies? ...
written 12 months ago by
roussine • 0
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... Hello!
can someone please give an opinion: does that make sense to merge PE reads before a de novo RNA-seq assembly (say with Trinity)?
Merging tools are quite fast (like USEARCH www.drive5.com/usearch/manual/merge_pair.html), and the amount of raw data is reduced drastically. Can merged data be sui ...
written 12 months ago by
roussine • 0
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... Hi Puli, thanks for the reply.
In the first place, the prog outputs a binary representation of a character (-) that it does not find in the conversion table (\00).
Ok, I can get things out of the binary into text, but a neater way would be to introduce a new character in the table, so that the cons ...
written 15 months ago by
roussine • 0
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... Thank you, gorgeous and simple tool, did not come across it before.
Can I please ask you. It uses the IUPAC table for making substitutions for the consensus, and the system table is:
# IUB codes for proteins
# Substitution is for OR'd A=1, C=2, D=4 etc.
#
A 1 A alanine
B 2052 DN ...
written 15 months ago by
roussine • 0
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... Hello folks,
can you think of any existing tool that would take a bunch of seqs in a protein fasta that ARE already ALIGNED and just merge those in a sort of a chimera-concatenate. Pieces might not overlap, and mismatches would produce X's or smth.. Like in this simple example.
>.. A ...
written 15 months ago by
roussine • 0
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... Hello folks,
will be grateful for your comment. Maybe someone had come across this.
I am observing a strange behavior of jellyfish: it hangs on a multi-core server (in a Trinity pipeline), basically stops using CPUs and runs forever. The pipeline is in a VirtualBox Ubuntu 14.0 (BioLinux 8). I canno ...
written 22 months ago by
roussine • 0
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