User: Anand Rao

gravatar for Anand Rao
Anand Rao100
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100
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Trusted
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United States
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2 days, 1 hour ago
Joined:
6 years ago
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Posts by Anand Rao

<prev • 84 results • page 1 of 9 • next >
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Comment: C: How to measure NGS depth coverage bias
... You've got > stats= flag twice, so could you have meant `out=covstats.txt`? ...
written 2 days ago by Anand Rao100
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How to measure NGS depth coverage bias
... Is there a software tool that reports a measure of the **degree of non-uniformity** in depth of Illumina sequencing coverage across a *de novo* assembled genome (against which the Illumina reads are mapped back)? I have the PE read library (2*150bp HiSeq4000), the *de novo* assembled genome, and th ...
illumina ngs bias sequencing depth coverage written 3 days ago by Anand Rao100 • updated 2 days ago by Len Trigg880
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Comment: C: primer design to discriminate sequences in intron-exon MSA
... Thanks Kevin. No need to apologize, especially when you are helping :) And help you did: some digging revealed an author of **Primique** to also be the author of **GeMprospector** = Jakob Fredslund. I've e-mailed him seeking pointers about which tools that can help me. I'll update this post when I h ...
written 8 days ago by Anand Rao100
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Comment: C: primer design to discriminate sequences in intron-exon MSA
... > Assuming that you know the exact sequences that you want to target Actually I do not, and eyeballing 3000 alignments to identify primer annealing sites is not feasible. While I appreciate your inputs, I am looking for suggestions to identify the primer annealing regions 1st - that will also ...
written 9 days ago by Anand Rao100
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primer design to discriminate sequences in intron-exon MSA
... I seek advice in the form a bioinformatics strategy to design primers to distinguish 10 sequences from one another. These 10 sequences are genic sequences, and across which their respective exonic sequences are highly conserved, and so is the number of exons. Their non-exonic sequences, as expected ...
msa primer intron-exon written 9 days ago by Anand Rao100 • updated 9 days ago by Kevin Blighe1.2k
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Answer: A: REAPR run error
... The reasons for this error is straightforward: The input file format/extension for this step of reapr has to be *.fastq and not *.gz (as I understand it) I consider this solved... ...
written 11 days ago by Anand Rao100
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REAPR run error
... I am running REAPR version 1.0.18 (and also the older 1.0.17) to check for correctness of my genome assemblies. However, I am getting a run error with the "**smaltmap**" step, and this error suggests that the input files are not in the correct format. Syntax used was: reapr smaltmap a5miseq_Et ...
reapr run error smalt written 12 days ago by Anand Rao100
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a5miseq syntax help
... Using instructions at https://sourceforge.net/p/ngopt/wiki/A5PipelineREADME/, I am opting to specify library files for my a5miseq runs. But I am getting errors, may be someone can tell me what is wrong with my run syntax? Details below. Thanks! 2 specific questions: **1.** when using a custom ada ...
a5miseq syntax fastq format custom adapters written 15 days ago by Anand Rao100 • updated 15 days ago by genomax33k
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Comment: C: Assembler for large genome de novo assembly with Illumina paired end reads of 15
... > You can feed Allpaths the short library again instead of a long > library, or you can assemble the short library with something like > Velvet and generate synthetic LMP reads from the contigs, which is the > approach we take. Is there a recommendation for which option might work bette ...
written 16 days ago by Anand Rao100
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A5 pipeline begin and end
... I have PE HiSeq4000 data that has been already trimmed using Trimmomatic, and Error Corrected using allpaths-LG. What would be my syntax for a5miseq? My understanding is that I should use --begin=2 --end=5, since I am starting beyond pre-processing step 1, but I want fully assembled contigs and as ...
assembler a5 pipeline genome assembly written 19 days ago by Anand Rao100

Latest awards to Anand Rao

Scholar 11 days ago, created an answer that has been accepted. For A: REAPR run error
Voter 12 days ago, voted more than 100 times.
Supporter 5 weeks ago, voted at least 25 times.
Popular Question 7 weeks ago, created a question with more than 1,000 views. For map gene gain loss on species tree
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Popular Question 12 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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