User: Torst
Torst • 950
- Reputation:
- 950
- Status:
- Trusted
- Location:
- Australia
- Website:
- http://www.bioinformat...
- Last seen:
- 4 months ago
- Joined:
- 8 years, 2 months ago
- Email:
- t**************@gmail.com
Microbial bioinformatics, *-omics.
Posts by Torst
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... `Score.value.real` suggests maybe you should add an `-evalue 1E-3` or something?
As an aside, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848038/ is a good article on matrices for short queries.
...
written 5 months ago by
Torst • 950
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... This one seems to be in the VCF 4.2 standard:
`##INFO=`
But as you say, the software using it may not be following the rules. Usually something like `-1` would be used to mean "no information" or "error". ...
written 5 months ago by
Torst • 950
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Comment:
C: awk extract certain line
... In Linux `dos2unix excel.txt` will fix the Windows line endings to be Unix compatible. ...
written 5 months ago by
Torst • 950
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... If your consensus accuracy is 99.9% then you still have 1 errors every 1000 bp. A typical bacterial gene is ~ 1000bp long. That 1 error is usually an indel. This results in a frame-shift in your CDS. If you use a gene finder like Prodgial (used in prokka) then you will get ~2 predicted CDS for eve ...
written 5 months ago by
Torst • 950
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... What minimum contig size did you include in that plot? ...
written 5 months ago by
Torst • 950
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... Spades often has trouble with 250bp PE reads.
I wrote Shovill to resolve this problem: https://github.com/tseemann/shovill
In your case I think however you have 1000s of TINY contigs.
You need to remove all the small contigs first to fix the N50 statistic.
`seqtk seq -L 500 contigs.fa > good_cont ...
written 5 months ago by
Torst • 950
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... This fails: rm -fr foo && ./minia -in ~/tmp/R1.fastq -out-dir foo
This works: mkdir foo && ./minia -in ~/tmp/R1.fastq -out-dir foo
If 'foo' doesn't exist it spits LOTS of messages like this:
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
#000: /home/vagrant/gatb-tools/gat ...
written 4.1 years ago by
Torst • 950
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... Is this some issue with assumption of hdf5 library being installed at system level instead of using bundled one?
cd /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/src && /bio/linuxbrew/bin/g++-5 -Os -w -pipe -march=core2 -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-So ...
written 4.1 years ago by
Torst • 950
• updated
4.1 years ago by
Rayan Chikhi • 1.4k
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Answer:
A: net charge of my protein
... EMBOSS has a "pepstats" tool to do this:
http://emboss.bioinformatics.nl/cgi-bin/emboss/help/pepstats
You can do it online here:
http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
...
written 5.5 years ago by
Torst • 950
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... A 6-mer is a subsequence of 6 letters (nucleotides or amino-acids).
For example, a length 10 DNA sequence has 5 possible 6-mers: the sequences using bases 1..6, 2..7, 3..8, 4..9, and 5..10. Think of a sliding window of length 6 moving across the sequence one letter at a time.
Aligning two sequenc ...
written 5.5 years ago by
Torst • 950
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For A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
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For Samtools / Bcftools Missing Random Obvious Single Base Indels
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For minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
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For A: Bacterial Genomes To Download
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For A: Blast Can'T Find Databases
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For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
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For Samtools / Bcftools Missing Random Obvious Single Base Indels
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For A: How To Blast A Sequence Against Multiple Databases
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For A: Blast Can'T Find Databases
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For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
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