User: Ada

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Ada10
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Posts by Ada

<prev • 36 results • page 1 of 4 • next >
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gsnap vs bbmap
... My gsnap alignment scores were much lower (77% vs 95%) than scores received from BBMAP. How can I go about rectifying this problem? ...
assembly alignment sequencing written 3 days ago by Ada10
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Purpose of genomescope/preliminary analysis of unassembled raw reads
... What is the ultimate purpose of using genomescope prior to assembly? I understand what genomescope does but why should it be done? ...
assembly alignment sequencing written 3 days ago by Ada10
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Comment: C: gsnap not producing sam files with header
... My files were in .fna.gz and that seemed to be the problem in producing SAM file with header. Converted to .fna and works fine now. ...
written 5 days ago by Ada10
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ALT <*> Interpretation
... In https://samtools.github.io/hts-specs/VCFv4.2.pdf ALT - alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or an angle-bracketed ID ...
indels alignment snp assembly written 5 days ago by Ada10
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Comment: C: Determine Insertion and/or Deletions from Extracted Indels
... I found my answer on page 9 of https://samtools.github.io/hts-specs/VCFv4.2.pdf ...
written 5 days ago by Ada10
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Determine Insertion and/or Deletions from Extracted Indels
... After extracting Indels from variants file, how does one determine/discern which are insertions and which are deletions? ...
gene indels snp sequencing written 5 days ago by Ada10
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Understanding SNP variant output
... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT What does the REF and ALT refer to in extraction of variants? ...
assembly alignment sequencing written 10 days ago by Ada10 • updated 10 days ago by reza.jabal420
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Comment: C: gsnap not producing sam files with header
... I am going to debug and follow up ...
written 12 days ago by Ada10
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Comment: C: gsnap not producing sam files with header
... There is no header at all ...
written 14 days ago by Ada10
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Comment: C: gsnap not producing sam files with header
... I made the correction and received this: [main_samview] fail to read the header from test1.sam file So it looks like the error is coming from the mapping to output .SAM file command. The correction of -h to the SAM to BAM file conversion states that their is also failure for reading header in .BA ...
written 14 days ago by Ada10

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