User: aindap

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aindap110
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7 months, 1 week ago
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6 years, 7 months ago
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I'm a tall drink of water. I like human genetics, Python, swimming, and the Phoenix Suns.

Posts by aindap

<prev • 15 results • page 1 of 2 • next >
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Answer: A: finding contigs present in one assembly but missing from another
... Have you tried [Assemblytics][1]? You can use [Mummer][2] to align your two assemblies and then use Assemblytics to see the differences. [1]: http://assemblytics.com/ "Assemblytics" [2]: http://mummer.sourceforge.net/ ...
written 8 months ago by aindap110
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GeneSCF and P-value Benjamini and Hochberg (FDR)
... Dumb question about the GeneSCF output. If I'm using the P-value Benjamini and Hochberg (FDR) column, would I choose an FDR cut point and take any rows with a BH P-value less than this value as significant? Thanks so much. ...
genescf written 13 months ago by aindap110 • updated 13 months ago by EagleEye5.6k
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Error correcting PacBio reads prior to alignment with bwa mem
... I have PacBio reads of my organism of interest that I would like to align to a reference sequence pulled from GenBank. Does it make sense to error correct and trim the PacBio reads, with a tool like [canu][1] and then align with bwa mem? [1]: http://canu.readthedocs.io/en/latest/index.html ...
bwa pacbio written 18 months ago by aindap110 • updated 18 months ago by Charles Warden5.2k
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Aligning de-novo assembly to reference strain genome
... Dear Biostars Community - I generated a de-novo assembly of my viral strain. I wanted to analyze differences of my denovo result to a reference strain, so got a very useful report from [Assemblytics][1] in conjunction with using the [nucmer][2] program from MUMmer. However the output of the alignme ...
multiple sequence alignment denovo assembly written 19 months ago by aindap110 • updated 11 months ago by asur0
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Comment: C: denovo-assembly with novel genes inserted
... Thank you so much!!! tadpole worked much *faster* and I got longer contigs The bbmap step helped me find the insert point of my novel genes in the virus I'm new to assembly, but this pipeline was just what I was looking for. ...
written 19 months ago by aindap110
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denovo-assembly with novel genes inserted
... I have a viral strain with non-viral sequences inserted in. I aligned to my reads to a reference strain. The reads that didn't align, I did a denovo assembly with SSAKE to identify my contigs of my non-viral sequences. What I want is a final assembly of my virus strain where I know the non-viral ...
assembly denovo assembly ilumina written 19 months ago by aindap110 • updated 19 months ago by Brian Bushnell15k
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what do read with blue outline represent in IGV?
... Dumb question, but I can't seem to find the answer in the IGV docs. I am unable to upload a screenshot due to restrictions, but I am viewing my alignments of Illumina PE reads aligned with BWA mem. Do the reads with a blue outline indicate improper insert size? ...
alignment igv written 19 months ago by aindap110 • updated 19 months ago by Biomonika (Noolean)3.0k
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finding repeats in de-novo assembled contig from PacBio reads
... Dear BioStars Community: I performed a de-novo assembly of PacBio reads using [Canu][1] for a viral genome. I have my resulting unitig from the canu pipeline. I am now interested in characterizing repeats in my resulting assembly. I'm new to assembly and repeat identification. One simple approach ...
assembly repeat pacbio written 20 months ago by aindap110 • updated 18 months ago by arnstrm1.7k
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Answer: A: Analyses With Case-Only Exomes
... Is this for a Mendelian or complex trait? ...
written 5.1 years ago by aindap110
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Answer: A: Concordance Between Ngs Snp Calls And Genotype Snp Arrays
... Have a look at VariantEval in the GATK, in particular using the -goldStandard argument. You can provide a VCF containing your SNP array genotypes as the gold standard to compare your sequencing derived VCF to. ...
written 5.4 years ago by aindap110

Latest awards to aindap

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Read Simulation With Mason - Snp Positions
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Interleaving Records From More Than One Fasta File
Autobiographer 5.0 years ago, has more than 80 characters in the information field of the user's profile.
Student 5.5 years ago, asked a question with at least 3 up-votes. For Interleaving Records From More Than One Fasta File

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