User: ram.mainali

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ram.mainali10
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Posts by ram.mainali

<prev • 9 results • page 1 of 1 • next >
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De-novo assembly using SPADES
... Before, I used SOAPdenovo2 to assemble my target reads. In order to use multiple k-mer and have better assembly result, I used SPADES for de-novo assembly using following commands SPAdes-3.9.1-Linux/bin/spades.py -1 insert_seq.JV18.k19_R1.fq -2 insert_seq.JV18.k19_R2.fq -t 2 -m 100 -o spades.J ...
assembly next-gen sequencing written 5 months ago by ram.mainali10 • updated 5 months ago by genomax47k
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SNPs mining using freebayes: problem in using multiple bam file of different ploidy
... My objective is to identify the SNPs on resistance gene/haplotype. I have resistance specific haplotype read and mapped bam file (ploidy = 1), susceptible haplotype read and mapped bam file (ploidy = 1) and other 9 susceptible varieties read and their mapped bam file (each variety with ploidy =4). ...
alignment next-gen snp written 6 months ago by ram.mainali10
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How to set coverage or cut-off on GenomeTester4/Glistcompare
... I produced list of kmers from WGS data which have coverage above a certain threshold or cut-off by using GenomeTester4 glistcompare. The command is: *GenomeTester4/bin/glistcompare inputfile.list inputfile.list -i -c 15 -o output* Besides setting coverage above a certain threshold (cut-off), here ...
genome next-gen glistcompare genometester4 written 7 months ago by ram.mainali10
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Comment: C: Insert size calculation for de-novo assembly
... Hi, h.mon. According to tutorial, first I used 450 as initial insert size and followed the procedure in Linux and R. Finally I obtained insert size of 322.72. Do you mean I can use 322.72 now for final assembly? Thank you ...
written 7 months ago by ram.mainali10
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Comment: C: Insert size calculation for de-novo assembly
... Thank you for your kind information ...
written 7 months ago by ram.mainali10
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Comment: C: Insert size calculation for de-novo assembly
... Thank you Sej Modha. Still I am wondering which value to use, 450 (from method information) or 322.72 from Linux+R studio calculation. Does the difference in value affect the quality of assembly? ...
written 7 months ago by ram.mainali10
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Insert size calculation for de-novo assembly
... The DNA of my experiment was fragmented using sonification with Covaris LE220 and expected DNA fragment length is 450 bp, which I expect the average insert size for SOAP configuration file. When I calculated average insert size of my specific region of interest by using the information provided in h ...
R de-novo assembly next-gen soap configuration written 7 months ago by ram.mainali10
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Calculation of signal-to-noise ratio (SNR)
... How can I calculate signal-to-noise ratio for example in graph showing k-mers peaks against chromosome bin. Is there good paper describing methods regarding calculation of signal-to-noise ratio (SNR) in the field of bio-bioinformatics or genomics. Thank you ...
genome next-gen snr sequencing written 8 months ago by ram.mainali10 • updated 8 months ago by Kevin Blighe19k
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K-mer size and de-novo assembly and SNP mining
... I have Illumina whole genome paired end short sequence reads of length 150 bp. I want to design k-mer, apply de-novo assembly and identify the SNPs markers. My questions are 1. What sizes of k-mer I should design. Do I need to design k-mer from both sides. 2. Which software do you think better f ...
genome next-gen de-novo assembly sequence snp written 9 months ago by ram.mainali10 • updated 9 months ago by WouterDeCoster28k

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