User: Tonor

gravatar for Tonor
Tonor420
Reputation:
420
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Trusted
Location:
UK
Last seen:
6 months ago
Joined:
2 years ago
Email:
r***********@hotmail.com

Posts by Tonor

<prev • 121 results • page 1 of 13 • next >
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Comment: C: Generate consensus sequence from BAM without ambiguity codes
... Brilliant thanks for that ...
written 6 months ago by Tonor420
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Comment: C: Generate consensus sequence from BAM without ambiguity codes
... Consensus Fixer looks great - thanks very much ...
written 6 months ago by Tonor420
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Generate consensus sequence from BAM without ambiguity codes
... To generate a consensus sequence from a BAM file I use the command: samtools mpileup -uf REF BAM | bcftools call -c | vcfutils.pl vcf2fq > SEQ samtools/vcfutils gives ambiguity codes when there is a mixed base population at a site, even if the secondary base is quite a low frequency (say 20 ...
sequence written 6 months ago by Tonor420 • updated 6 months ago by swbarnes24.0k
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Comment: C: Identifying mutations in an aligment
... Thanks - I was going to write something - but thought there would be something already out there ...
written 6 months ago by Tonor420
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Comment: C: Identifying mutations in an aligment
... Hi - this is not NGS data - so not SAM/BAM just a standard FASTA alignment of aligned gene sequences ...
written 6 months ago by Tonor420
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Identifying mutations in an aligment
... Does anyone know of any tools that will identify the mutations present in an alignment? I have an alignment of hundreds of gene seqs (all closely related), the first sequence in the alignment is the "reference" sequence, and I want to identify and report mutations in the gene seqs with respect to t ...
alignment sequence written 6 months ago by Tonor420 • updated 6 months ago by a.zielezinski8.4k
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Tool to flip contigs the right orientation with respect to a reference sequence
... Does anyone know a tool(s) that can flip contigs generated from a de novo assembly so that they are the correct orientation with respect to a reference sequence? I have multiple contigs generated from de novo, blasting them identifies a few that match a particular species I'm interested in, I then ...
assembly sequence alignment written 6 months ago by Tonor420 • updated 6 months ago by h.mon19k
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Answer: A: BAM/SAM to aligned FASTA file
... To align your consensus sequence to your reference sequence you will need to use an alignment tool to create a multiple sequence alignment, such as: MAFFT, MEGA, CLUSTAL, and loads of others These tools don't care that one is a consensus, and one is reference, it just aligns all the sequences you ...
written 21 months ago by Tonor420
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Comment: C: TopHat2: "IOError: [Errno 28] No space left on device" with large input
... What operating system are you running on? And how is it set up - are there different partitions? What command are you using to run TopHat - specifically where are you directing the output to? How quickly does it give the error - straight away or after a while? 645GB capacity with a 250GB input FAST ...
written 21 months ago by Tonor420
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Comment: C: Error when running PhiSpy
... @brindha, you could maybe try: PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25 Or /Full/Path/To/Folder/PhiSpy.py -i Test_Organism/160490.1/ -o output_directory -t 25 ...
written 21 months ago by Tonor420

Latest awards to Tonor

Popular Question 17 months ago, created a question with more than 1,000 views. For Remove Duplicate Reads from paired end data set
Centurion 21 months ago, created 100 posts.
Rising Star 22 months ago, created 50 posts within first three months of joining.
Teacher 22 months ago, created an answer with at least 3 up-votes. For C: Cannot find downloaded files from SRA toolkit (prefetch)

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