User: DK

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DK70
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Canada
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Posts by DK

<prev • 119 results • page 1 of 12 • next >
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Comment: C: How to get a consensus of the contigs obtained from an assembler like spades?
... Thanks for your comments! With separating the reads it gives better contig results because apparently the assembler algorithms perform better with small chunk of reads. ...
written 2 days ago by DK70
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How to get a consensus of the contigs obtained from an assembler like spades?
... Dear Friends, I have assembled a phage (represented by a single fastq file) contigs using SPAdes. Reference phage genome is unknown. I divided the fastq file into separate files with 25000 reads each. Assembled the reads using Mira and Spades. Spades gave good results with the largest contig being ...
consensus spades contigs written 2 days ago by DK70
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Corrections of the peak areas of C13 isotopes of mass-spectrometry data using ICT package
... Dear Friends, I have mass-spec data for a 13C isotope for a compound: **note compound compoundId formula expectedRtDiff ppmDiff parent 091215_0i** C12 PARENT Acetyl CoA HMDB01206 C23H38N7O17P3S 0.004406929 0.7552748 808.1191 5367.899 C13-label-1 Acetyl CoA HMDB01206 C23H38N7O17P3S ...
c13 mass-spectrometry ict package written 4 days ago by DK70
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Comment: C: How to decide how many Iontorrent reads to run for contig assembly using Mira as
... Thanks genomax! If I have to do normalization, then should I do it on the main fastq file with 180000 reads? or the fastq files generated from the main fastq files with reads like 10000, 20000 etc? I would really appreciate your suggestion on this and the rational behind the selection. Thanks much! ...
written 11 days ago by DK70
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How to decide how many Iontorrent reads to run for contig assembly using Mira assembler?
... Dear Friends, I am running Mira contig assembler on a iontorrent sequenced bacteriophage fastq file. The total number of reads in the fastq file is about 1800000; the average read length in the fastq file is 300, and the reference genome is unknown. To run the program efficiently, I have divided ...
reads mira assembler iointorrent contigs written 11 days ago by DK70 • updated 11 days ago by WouterDeCoster35k
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Comment: C: How to Identify the pathogenicity of a set of variants (by using ACMG guidelines
... Thanks Fin! I am looking for computational approach to predict the pathogenicity of the variants in the vcf file using the ACMG guidelines. I am finding it hard to start, like what is the first step to implement? I know that vcf files contain SNP information and I should be looking at heterozygous a ...
written 13 days ago by DK70
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How to Identify the pathogenicity of a set of variants (by using ACMG guidelines)?
... Dear Friends, Am trying to find the pathogenicity of a set of variants (by using ACMG guidelines: https://www.ncbi.nlm.nih.gov/pubmed/25741868 ). The vcf file of the variants looks like this: CHROM POS ID REF ALT GT 22 11005678 . G A 0|1 ...
pathogenicity snp variants written 13 days ago by DK70 • updated 13 days ago by kuan-lin.huang10
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Where to get Epimatrix algorithm from for epitope binding prediction?
... Dear Friends, Can you please let me know where to obtain Epimatrix algorithm ( from iVAX) from for epitope binding prediction? I came across many references but did not find any medium to download or use it. Thanks. DK ...
hla epimatrix epitope written 16 days ago by DK70 • updated 16 days ago by Joseph Hughes2.6k
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Comment: C: SPAdes output with assembling warning
... Hi, Thanks for your previous helpful comments! I have got the contigs from spades and now looking to get the coverage. I have got this below result by using "bbmap.sh" on my data to get the coverage. Could you please tell me how to interpret the coverage here? Average coverage shown here is 209.654 ...
written 24 days ago by DK70
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Comment: A: How do I access genome coverage using SPADES?
... Hello All, This post was useful - thanks! I have got this result by using bbmap.sh on my data. Could you please tell me how to interpret the coverage here? Average coverage is 209.654 - what does this mean? I would really appreciate your input. Genome: 1 Key Length: ...
written 24 days ago by DK70

Latest awards to DK

Centurion 4 months ago, created 100 posts.
Supporter 8 months ago, voted at least 25 times.

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