User: Dr.Animo
Dr.Animo • 10
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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
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... @a.alnawfal I haven't FASTQ and Qual file. ...
written 5 weeks ago by
Dr.Animo • 10
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... 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 ...
written 5 weeks ago by
Dr.Animo • 10
• updated
5 weeks ago by
a.alnawfal.1992 • 40
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... Thanks for the response.
I've fixed it the problem is due to `expt` ...
written 5 months ago by
Dr.Animo • 10
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... 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 ...
written 5 months ago by
Dr.Animo • 10
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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.Animo • 10
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C: viral genome assembly
... I could not find any major difference by applying `mindepth`
...
written 7 months ago by
Dr.Animo • 10
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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.Animo • 10
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5 follow
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... 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 ...
written 7 months ago by
Dr.Animo • 10
• updated
7 months ago by
Mensur Dlakic • 5.8k
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... 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. ...
written 19 months ago by
Dr.Animo • 10
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