User: Anand Rao

gravatar for Anand Rao
Anand Rao150
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150
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United States
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an hour ago
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6 years, 10 months ago
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Posts by Anand Rao

<prev • 95 results • page 1 of 10 • next >
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collapsing GFF coordinates with common start OR stop
... I have inherited some GFF files where identified features often have common start or stop coordinates. I need to collapse such occurrences to the longest instance. As examples, I have provided an example problem and the solution below. Are there readily available tools that can do this? OR someone's ...
bedtools perl gff parse script written 18 hours ago by Anand Rao150 • updated 17 hours ago by h.mon16k
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Simulating Core / Accessory genome for incomplete genome assemblies
... I am looking to infer core and accessory genomes for ~ 300 fungal strains of the same species. Their drafts are of different build quality. One goal is to try and make predictions for how many core and accessory genes may be missing from each of my draft genomes, based on how many conserved genes a ...
simulation core accessory incomplete draft written 9 months ago by Anand Rao150
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Comment: C: Best mapping software to generate BAM file
... bwa-mem appears to have no flag to specify how many maximum numbers of mismatches are allowed, someone please correct me if I am mistaken. Regardless, for bbmap.sh, what would that flag be, to specify max. no. of mismatches? My university HPCC is inaccessible because of generator test - so I am un ...
written 9 months ago by Anand Rao150
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Comment: C: Best mapping software to generate BAM file
... Not replicating prior results any more, good memory https://www.biostars.org/u/18713/. Thanks to useful inputs from forum members, including yourself, I've figured why and how I was able to improve upon prior results in terms of contiguity (QUAST, no reference) and completeness (BUSCO) - I'm now wor ...
written 9 months ago by Anand Rao150
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Best mapping software to generate BAM file
... I have the following tasks that I need to carry out **a.** BAM mapping of Illumina HiSeq 4000 paired end 2*150bp reads to *de novo* assembly inferred from those reads, **b.** Sort BAM file by coordinates, **c.** Index BAM file, **d.** Mark or Remove Duplicates in BAM file. When I was looking in ...
bam mapping written 9 months ago by Anand Rao150 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Assess and correct any GC bias in Illumina HiSeq 4000 data
... Indeed, Brian, I have tried your assemblyPipeline.sh steps apart from other combinations of (assemblers+pre-processing steps). Each time, I obtain REAPR results that indicate mis-assemblies and mis-joints that should really be gaps - on the order of 80-90K, for each of my tested *de novo* assembly ...
written 9 months ago by Anand Rao150
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Assess and correct any GC bias in Illumina HiSeq 4000 data
... I am using REAPR software to assess correctness of my *de novo* genome assembly from HiSeq4000 Illumina reads - this software simply compares theoretical predictions of uniform coverage to actual observed coverage based on mapping component reads back to the inferred assembly. The coverage Vs GC plo ...
hiseq 4000 illumina gc bias coverage depth written 9 months ago by Anand Rao150 • updated 9 months ago by Brian Bushnell15k
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Comment: C: Illumina R1 vs. R2 read quality differences - reasons?
... Thanks https://www.biostars.org/u/18713/ ...
written 10 months ago by Anand Rao150
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Illumina R1 vs. R2 read quality differences - reasons?
... I am trying to understand the theoretical bases and practical causes for why R2 is poorer quality compared to R1 for Illumina Paired End sequencing. While there are some posts here that discuss this observation: https://www.biostars.org/p/99138/ https://www.biostars.org/p/198243/ what I am most i ...
illumina read quality pe written 10 months ago by Anand Rao150 • updated 10 months ago by Istvan Albert ♦♦ 77k
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Comment: C: Assessment of de novo genome assembly accuracy ?
... https://www.biostars.org/u/23936/ - Were you able to successfully use REAPR for your analyses? I am trying to use REAPR to assess de novo assembly correctness, but am encountering some rather strange errors/warnings results, hence this question. Thanks! ...
written 10 months ago by Anand Rao150

Latest awards to Anand Rao

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Database for plant ploidy
Popular Question 9 weeks ago, created a question with more than 1,000 views. For map gene gain loss on species tree
Popular Question 8 months ago, created a question with more than 1,000 views. For tools for Reciprocal BLAST hit processing
Popular Question 8 months ago, created a question with more than 1,000 views. For Database for plant ploidy
Popular Question 9 months ago, created a question with more than 1,000 views. For map gene gain loss on species tree
Scholar 10 months ago, created an answer that has been accepted. For A: REAPR run error
Voter 10 months ago, voted more than 100 times.
Supporter 11 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For map gene gain loss on species tree
Popular Question 15 months ago, created a question with more than 1,000 views. For Running High-Throughput Searches Using Wise2 Software
Popular Question 23 months ago, created a question with more than 1,000 views. For Accelerating BLAST for million sequence BLASTp all-by-all

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