User: roussine

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Posts by roussine

<prev • 8 results • page 1 of 1 • next >
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Comment: A: Convert tree confidence values to integers
... Alex - thanx indeed for this advice ...
written 12 months ago by roussine0
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Convert tree confidence values to integers
... 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. ...
confidence tree bootstrap written 12 months ago by roussine0
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Comment: C: Merging PE reads before de novo RNA-Seq assembly
... 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 roussine0
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Merging PE reads before de novo RNA-Seq assembly
... 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 ...
usearch assembly rna-seq pe reads written 12 months ago by roussine0
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Comment: C: Making seq chimeras and concatenation in protein MSAs
... 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 roussine0
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Answer: A: Making seq chimeras and concatenation in protein MSAs
... 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 roussine0
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Making seq chimeras and concatenation in protein MSAs
... 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 ...
consensus consambig alignment emboss concatenation written 15 months ago by roussine0
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Jellyfish stalls on a multi-CPU server (Trinity pipe)
... 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 ...
trinity rna-seq jellyfish written 22 months ago by roussine0

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