User: andrew.j.skelton73

Reputation:
3,110
Status:
Trusted
Location:
Newcastle Upon Tyne
Last seen:
9 hours ago
Joined:
3 years, 4 months ago
Email:
a*****************@gmail.com

about me

Posts by andrew.j.skelton73

<prev • 511 results • page 1 of 52 • next >
0
votes
1
answer
2.0k
views
1
answers
Comment: C: retrieve normalised count data from DESeq2
... Yes, or don't include the `normalized` parameter as when you look at the function's help page (`?DESeq2::counts`), you'll see that it's `FALSE` by default. ...
written 2 days ago by andrew.j.skelton733.1k
2
votes
1
answer
139
views
1
answers
Answer: C: Merging stringtie assemblies using stringtie merge
... This depends on your hypothesis, but the idea generally is to merge all assembled transcriptomes, so that you have an "experiment-wide transcriptome", rather than stratifying. ...
written 5 weeks ago by andrew.j.skelton733.1k
1
vote
3
answers
186
views
3
answers
Answer: A: CNV detection techniques, algorithms, applications ...
... If you're looking for somatic copy number events in exome data, check out [GATK's best practises][1] Edit: I just noticed that GATK basically refer you to the workshop docs in that link (Super helpful, I know). In any case, [here's the relevant doc][2] [1]: https://software.broadinstitute.org/g ...
written 5 weeks ago by andrew.j.skelton733.1k
3
votes
2
answers
119
views
2
answers
Answer: A: How can I only took the mapped ones from STAR ?
... To get your mapped reads: samtools view -b -F 4 alignment.bam > mapped.bam To get your unmapped reads: samtools view -b -f 4 alignment.bam > unmapped.bam The `-f` filters based on bitwise samflags. Flag 4 (or `0x0004`) is for unmapped reads. `-F` does the inverse. ...
written 5 weeks ago by andrew.j.skelton733.1k
0
votes
0
answers
201
views
0
answers
Comment: C: Warning encountered while transcript abundance estimation using stringtie
... Are the entries in the gff file synonymous with the annotation of the fasta files you used to build the HISAT index? ...
written 5 weeks ago by andrew.j.skelton733.1k
0
votes
0
answers
201
views
0
answers
Comment: C: Warning encountered while transcript abundance estimation using stringtie
... Have you [checked][1] your gff3 file looks valid? Also was this the `reference.gff3` used in your original alignment? [1]: http://ccb.jhu.edu/software/stringtie/gff.shtml ...
written 5 weeks ago by andrew.j.skelton733.1k
1
vote
1
answer
162
views
1
answers
Comment: C: how to incorporate the gene ids/in tophat query
... > Need quick response please. Your question is no more a priority than others. > using tophat Tophat has been replaced by [HISAT2][1], or you could use [STAR][2], both of which are perform far better than Tophat. Your question is unclear on how specifically you've done your counting, wh ...
written 6 weeks ago by andrew.j.skelton733.1k
0
votes
2
answers
128
views
2
answers
Comment: C: How to get IDs of family trios in 1000 genomes project?
... See [here][1] for an explanation of the ped (pedigree) file. [1]: http://www.gwaspi.org/?page_id=145 ...
written 7 weeks ago by andrew.j.skelton733.1k
1
vote
0
answers
187
views
0
answers
Comment: C: how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
... I wouldn't normally suggest this, but I think you'd have a better shot on [Bioconductor support][1], as Kasper Hansen is on that mailing list when Minfi is tagged. No doubt Kasper would be able to give you a solid answer. Try to link to the post for future users. Edit: I see you've already [done t ...
written 7 weeks ago by andrew.j.skelton733.1k
0
votes
1
answer
131
views
1
answers
Comment: C: How to compute global chromosome expression from RNA-Seq
... bowtie2 is not splice aware. ...
written 7 weeks ago by andrew.j.skelton733.1k

Latest awards to andrew.j.skelton73

Scholar 2 days ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Student 11 weeks ago, asked a question with at least 3 up-votes. For 450K - "Best" Normalisation Method?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Scholar 12 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Scholar 12 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Scholar 3 months ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Scholar 3 months ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Popular Question 6 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams
Popular Question 7 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams
Popular Question 7 months ago, created a question with more than 1,000 views. For Using biomaRt to find the nearest upstream/ downstream gene from an Ensembl ID
Popular Question 8 months ago, created a question with more than 1,000 views. For Using biomaRt to find the nearest upstream/ downstream gene from an Ensembl ID
Popular Question 9 months ago, created a question with more than 1,000 views. For Illumina Microarray Annotation
Scholar 9 months ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Popular Question 10 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 423 users visited in the last hour