User: Torst

gravatar for Torst
Torst950
Reputation:
950
Status:
Trusted
Location:
Australia
Website:
http://www.bioinformat...
Last seen:
4 weeks ago
Joined:
7 years, 11 months ago
Email:
t**************@gmail.com

Microbial bioinformatics, *-omics.

Posts by Torst

<prev • 100 results • page 1 of 10 • next >
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Comment: C: NCBI blastp fails with "Invalid choice selection: NCBI-Seqalign::Score.value.rea
... `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 9 weeks ago by Torst950
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Comment: C: Not understand the value in VCF file
... 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 9 weeks ago by Torst950
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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 9 weeks ago by Torst950
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Comment: C: High CDS Count in my assembled Genome using Nanopore reads (ONT) data
... 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 9 weeks ago by Torst950
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Comment: C: Understanding coverage in genome assemblies
... What minimum contig size did you include in that plot? ...
written 9 weeks ago by Torst950
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Answer: A: Varying assembly statistics: Abyss & SPades
... 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 9 weeks ago by Torst950
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(Closed) Minia 2.0.3 binary spits out lots of HDF5 errors if -out-dir doesn't exit
... 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 ...
minia written 3.9 years ago by Torst950
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minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
... 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 ...
minia written 3.9 years ago by Torst950 • updated 3.9 years ago by Rayan Chikhi1.4k
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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 5.2 years ago by Torst950
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Answer: A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
... 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 5.2 years ago by Torst950

Latest awards to Torst

Scholar 9 weeks ago, created an answer that has been accepted. For A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
Guru 9 weeks ago, received more than 100 upvotes.
Popular Question 11 months ago, created a question with more than 1,000 views. For Samtools / Bcftools Missing Random Obvious Single Base Indels
Popular Question 11 months ago, created a question with more than 1,000 views. For minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
Scholar 3.0 years ago, created an answer that has been accepted. For A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
Scholar 3.0 years ago, created an answer that has been accepted. For A: Bacterial Genomes To Download
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Samtools / Bcftools Missing Random Obvious Single Base Indels
Good Answer 4.7 years ago, created an answer that was upvoted at least 5 times. For A: Blast Can'T Find Databases
Appreciated 4.7 years ago, created a post with more than 5 votes. For A: Blast Can'T Find Databases
Good Answer 4.7 years ago, created an answer that was upvoted at least 5 times. For A: How To Blast A Sequence Against Multiple Databases
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: Blast Can'T Find Databases
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
Supporter 5.5 years ago, voted at least 25 times.
Student 6.0 years ago, asked a question with at least 3 up-votes. For Samtools / Bcftools Missing Random Obvious Single Base Indels
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Visualization Of Sequencing Data From Bacteria (Prokaryotes)
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: How To Blast A Sequence Against Multiple Databases
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: Blast Can'T Find Databases
Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?

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