User: ####

gravatar for ####
####140
Reputation:
140
Status:
Trusted
Location:
Last seen:
4 weeks, 1 day ago
Joined:
2 years, 3 months ago
Email:
m************@gmail.com

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

Posts by ####

<prev • 94 results • page 1 of 10 • next >
0
votes
1
answer
161
views
1
answer
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 12 weeks ago by ####140 • updated 12 weeks ago by trausch760
1
vote
0
answers
188
views
0
answers
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 3 months ago by ####140
0
votes
1
answer
390
views
1
answers
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 4 months ago by ####140
0
votes
1
answer
390
views
1
answers
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 4 months ago by ####140
0
votes
1
answer
390
views
1
answers
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 4 months ago by ####140
0
votes
1
answer
390
views
1
answer
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 4 months ago by ####140
0
votes
1
answer
1.2k
views
1
answers
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 4 months ago by ####140
1
vote
2
answers
1.3k
views
2
answers
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 5 months ago by ####140
1
vote
2
answers
1.3k
views
2
answers
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 5 months ago by ####140
1
vote
2
answers
318
views
2
answers
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 6 months ago by ####140 • updated 6 months ago by Mike Smith300

Latest awards to ####

Scholar 10 months ago, created an answer that has been accepted. For A: IGV custom Genome
Autobiographer 10 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 18 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1771 users visited in the last hour