User: Dr.Animo

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Dr.Animo10
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10
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New User
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Last seen:
1 week, 1 day ago
Joined:
1 year, 7 months ago
Email:
m******@gmail.com

I am doing MS in Bioinformatics from COMSATS Islamabad. I have an interest in comparative genomics, metagenomics and sRNA identification by using in-silico methods. I have also some experience in these fields. I have also some experience in homology modeling of protein, motif analysis and data mining from the databases like NCBI, Ensembl and UCSC genome browser. 

Posts by Dr.Animo

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to calculate mutation rate and mutation sites in a genome using FASTA file?
... @a.alnawfal I haven't FASTQ and Qual file. ...
written 5 weeks ago by Dr.Animo10
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How to calculate mutation rate and mutation sites in a genome using FASTA file?
... Hi, I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format. I want to know, how I can identify mutations and mutation sites in those genomes using FASTA sequences (If I've FASTQ file then I'll simply align the reads to the reference and by using variant calling to ...
alignment mutation snp mutation rate written 5 weeks ago by Dr.Animo10 • updated 5 weeks ago by a.alnawfal.199240
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Comment: A: EdgeR Warning message In estimateCommonDisp.
... Thanks for the response. I've fixed it the problem is due to `expt` ...
written 5 months ago by Dr.Animo10
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EdgeR Warning message In estimateCommonDisp.
... Hi everyone, I am trying to perform DEG analysis. I've two samples each has 3 replicates (one is XR and other is YR) replicates are XR1,XR2,XR3 and YR1,YR2,YR3.. d<- DGEList(counts=as.matrix(raw.data[,2:7]), lib.size=library.sizes, group=expt) d<- calcNormFactors(d) At the following ...
R rna-seq edger deg written 5 months ago by Dr.Animo10
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Comment: C: viral genome assembly
... What about `V-GAP` assembly pipeline? https://www.sciencedirect.com/science/article/pii/S0378111915012378 I could not find the pipeline that proposes the author in the article. If someone has this then please share it. ...
written 7 months ago by Dr.Animo10
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Comment: C: viral genome assembly
... I could not find any major difference by applying `mindepth` ...
written 7 months ago by Dr.Animo10
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Comment: C: viral genome assembly
... I've already assembled the reads with tadpole, the number of contigs decreased but they are very high. mindepth=X What is X here? ...
written 7 months ago by Dr.Animo10
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viral genome assembly
... Dear all, I am trying to assemble a phage (virus) genome. I've checked the quality of the reads and mapped them to the host genome to remove the host genome reads. Now I am trying to assemble the unmapped reads but the number of contigs is more than 1000. I have tried different kmer sizes and differ ...
chimeric reads assembly virus genome written 7 months ago by Dr.Animo10 • updated 7 months ago by Mensur Dlakic5.8k
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unicycler assembly parameters
... Hi, I want to assemble the illumina reads by using unicycler. So, what parameters should I set for better assembly. I ran a example reads, which are alredy assemble. I want to compare the results. I set the default parameters, but the difference between result is very large. So, can you help me? 1. ...
assembly written 19 months ago by Dr.Animo10

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