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####130
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Bioinformatician, proficient in handling NGS & Micro-array data.
 

Posts by ####

<prev • 94 results • page 1 of 10 • next >
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Sequence uniformity cov
... I wan to generate sequence uniformity coverage plot like this :![enter image description here][1] any recommendation for package or tools other den `bamQC`/`multi-bamQC` & `TEQC`? I have multiple samples and i want to plot for all together. [1]: https://assets.illumina.com/content/dam/il ...
next-gen rna-seq sequencing written 4 weeks ago by ####130 • updated 27 days ago by trausch650
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Parsing augustus output
... I have performed gene model prediction using AUGUSTUS and I want to parse the output in the from of fasta file and gff/gtf file can any one suggest? ...
genome annotation gene prediction written 8 weeks ago by ####130
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Comment: C: QC of fast5 files
... I prefer STAR over GMAP as STAR gives more specific alignment and False positive rate is less using STAR then GMAP. and STAR has provided promising results on PacBio Long reads. ...
written 10 weeks ago by ####130
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Comment: C: QC of fast5 files
... Yes I'll let you know how it looks for my data.Its for RNA-Seq data , any particular consideration for RNA-Seq data ? ...
written 10 weeks ago by ####130
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Comment: C: QC of fast5 files
... Seems your **Nanoplot** shall do the needful. I am looking for something similar you have performed here : https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/ , the average read quality. As mentioned by you, you have performed : [Per base sequence content and quality][ ...
written 10 weeks ago by ####130
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QC of fast5 files
... I have fast5 files from Minion data. I want to perform the quality check for these files are there any tools available for Quality check of fast5 files? I tried an alternative I extracted fastq from fast5 and then tried to do fastqc,but results are not satisfactory quality scores are very low , I a ...
fastq minion fast5 written 10 weeks ago by ####130
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Comment: C: How to find intron co-ordinates from the gff file?
... Hi @Devon I was trying your above mentioned code and I am getting following errror: > > exons > GRangesList object of length 37989: > $ENSG00000000003 > GRanges object with 20 ranges and 2 metadata columns: > seqnames ranges strand | ...
written 12 weeks ago by ####130
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Answer: A: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... Hi thanks for your reply, clusterProfiler is not getting updated I have updated my R version to 3.4 and then installed ReactomePA & Clusterprofiler but I am getting the same old version of both the packages. Can anyone you now tell me what could be the solution for this? Here is the output of m ...
written 3 months ago by ####130
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Answer: A: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... I am using ReactomePA and my input looks like this,entrezId & p-value : > gene 433016 16365 16891 71816 170835 71738 100034251 14058 215257 245126 108078 20558 57248 16456 56619 17474 20288 64292 14727 71519 ...
written 3 months ago by ####130
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Ensembl Biomart Plant database
... I want to fetch Arabidospsis annotation via ensembl biomart R package, here is the example how I am trying to fetch it: library("biomaRt") species = athaliana db = useMart(biomart = "plants_mart",paste(species,"_eg_gene",sep=""), host = "plants.ensembl.org") features = ...
R bioconductor biomart written 4 months ago by ####130 • updated 4 months ago by Mike Smith220

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Scholar 8 months ago, created an answer that has been accepted. For A: IGV custom Genome
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