User: ####

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####190
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190
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1 year ago
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m************@gmail.com

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 2.1 years ago by ####190 • updated 2.1 years ago by trausch1.4k
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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 2.2 years ago by ####190 • updated 14 months ago by opplatek30
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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 2.2 years ago by ####190
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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 2.2 years ago by ####190
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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 2.2 years ago by ####190
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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 2.2 years ago by ####190
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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 2.2 years ago by ####190
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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 2.3 years ago by ####190
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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 2.3 years ago by ####190
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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 2.4 years ago by ####190 • updated 2.4 years ago by Mike Smith1.3k

Latest awards to ####

Popular Question 20 months ago, created a question with more than 1,000 views. For AGP file format
Popular Question 20 months ago, created a question with more than 1,000 views. For Augustus new species training
Popular Question 20 months ago, created a question with more than 1,000 views. For RepeatMasker for Fungi
Popular Question 20 months ago, created a question with more than 1,000 views. For 3D PCA Plot from RNA-Seq data
Popular Question 20 months ago, created a question with more than 1,000 views. For SAM/BAM file filtering
Popular Question 20 months ago, created a question with more than 1,000 views. For QC of fast5 files
Popular Question 20 months ago, created a question with more than 1,000 views. For GTF/GFF file for feature count
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to do gene enrichment analysis?
Popular Question 21 months ago, created a question with more than 1,000 views. For RepeatMasker for Fungi
Scholar 2.7 years ago, created an answer that has been accepted. For A: IGV custom Genome
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.
Supporter 3.3 years ago, voted at least 25 times.

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