User: Anand Rao

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Anand Rao210
Reputation:
210
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Trusted
Location:
United States
Last seen:
13 minutes ago
Joined:
7 years, 6 months ago
Email:
a*********@gmail.com

Posts by Anand Rao

<prev • 126 results • page 1 of 13 • next >
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RepeatModeler run error troubleshooting
... I believe I am having trouble with the BuildDatabase step (for some inputs, but not all) And that this is causing subsequent non-0 exit status of my runs I have described my errors at: https://github.com/rmhubley/RepeatModeler/issues/24 and to make sure my input file formatting and the modified sy ...
builddatabase blastdb repeatmodeler repeatmasker written 2 days ago by Anand Rao210
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Extract VCF from genome assemblies of multiple individuals
... Is it possible to extract SNP information into a VCF file, from ~ 20 **genome assemblies** of individuals from the same species, each about ~ 300MB in size? While this is routinely done with NGS reads, mapping them to a reference, my question is specifically how to achieve the end goal of the VCF f ...
vcf snp genomes alignment structural variation written 15 days ago by Anand Rao210
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Answer: A: Which NGS aligner to find inexact matches
... One possible piped solution to report inexact matches in a genome to fasta formatted queries = **BBmap (from BBtools) | sam2bed (from bedops)** See https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/ Steps and syntax that might be applicable for my case: **Step 1.** Bui ...
written 6 weeks ago by Anand Rao210
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Comment: C: BLAST run parameters and parsing advice
... I realized local alignment tools (such as BLASTn that use the Smith Waterman algo) are not the way to go, I need a global end-to-end alignment tool (like VMATCH or Bowtie2 that use the Needleman Wunsch algo) So I have to retract my question, since it's premise of using BLASTn is itself wrong! ha :} ...
written 6 weeks ago by Anand Rao210
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Comment: C: Which NGS aligner to find inexact matches
... I have to do the equivalent of `-perc_identity 0.8 -qcov_hsp_perc 0.8` because it has been done in past studies, though strangely using BLAST, not accounting for its local SW algo. I agree with your observation that I need a global aligner that uses the Needleman-Wunsch algo. However, I still need ...
written 6 weeks ago by Anand Rao210
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Comment: C: Which NGS aligner to find inexact matches
... I've used neither BWA not pysam, so could you share any code snippet, or links to any examples that will help me understand your suggestion correctly and quickly? Also, am I right in interpreting your response as BWA MEM reporting not just PERFECT matches, but other matches with < 100% identity ...
written 6 weeks ago by Anand Rao210
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Which NGS aligner to find inexact matches
... I have a set of 100 bp sequence queries (not sequence reads, but data from some analyses). I need to report coordinates in the genome, that match each of these sequences, but filtered in at **a.** >= 80% identity, and **b.** >= 80% query length coverage. I think BLAST, FASTA, BLAT - the ...
ngs dna alignment genome coordinates ngs aligner written 6 weeks ago by Anand Rao210
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Comment: C: BLAST run parameters and parsing advice
... Thanks Lieven. I've added an image and some lines in italics to help me visualize match cases better. Look fwd to your response. ...
written 6 weeks ago by Anand Rao210
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Comment: C: bedtools subtract still overlaps by 1bp?
... Crystal clear, thank you again for those simple, yet elegant examples...getfasta worked great with my bed files. ...
written 6 weeks ago by Anand Rao210
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(Closed) BLAST run parameters and parsing advice
... I have a set of transposon element(TE) sequences and their genomic coordinates. For each TE, I have concatenated a mosaic of their flanking 5' and 3' sequences, up to 50nt on each end, so up to 100nt total mosaic length. *Let's call this the "**pre-insertion**" sequence.* Now, for each mosaic as ...
blastparser blast blastn written 6 weeks ago by Anand Rao210

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Popular Question 15 days ago, created a question with more than 1,000 views. For Ideal sequence % identity for profile construction
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