User: andrew.j.skelton73

Reputation:
3,060
Status:
Trusted
Location:
Newcastle Upon Tyne
Last seen:
2 hours ago
Joined:
3 years, 2 months ago
Email:
a*****************@gmail.com

about me

Posts by andrew.j.skelton73

<prev • 510 results • page 1 of 51 • next >
0
votes
0
answers
71
views
0
answers
Comment: 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 4 days ago by andrew.j.skelton733.1k
1
vote
3
answers
140
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 4 days ago by andrew.j.skelton733.1k
3
votes
2
answers
92
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 days ago by andrew.j.skelton733.1k
0
votes
0
answers
139
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 6 days ago by andrew.j.skelton733.1k
0
votes
0
answers
139
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 6 days ago by andrew.j.skelton733.1k
1
vote
1
answer
128
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 using tophat Tophat has been replaced by [HISAT2][1], or you could use [STAR][2], both of which are perform far better than Tophat.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 12 days ago by andrew.j.skelton733.1k
0
votes
2
answers
102
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 18 days ago by andrew.j.skelton733.1k
1
vote
0
answers
137
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 19 days ago by andrew.j.skelton733.1k
0
votes
1
answer
103
views
1
answers
Comment: C: How to compute global chromosome expression from RNA-Seq
... bowtie2 is not splice aware. ...
written 20 days ago by andrew.j.skelton733.1k
1
vote
0
answers
73
views
0
answers
Comment: C: Is there any way of adjusting age in methylation 450k data?
... Instead of jumping into ComBat, have you tried adding the Age term in your model when doing differential methylation? Does that improve your number of differentially methylated probes? ...
written 20 days ago by andrew.j.skelton733.1k

Latest awards to andrew.j.skelton73

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Scholar 5 days ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Popular Question 8 days ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Popular Question 18 days ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Popular Question 20 days ago, created a question with more than 1,000 views. For Ensembl Gtf Cuffmerge Duplicates
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Commentator 29 days ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Student 7 weeks ago, asked a question with at least 3 up-votes. For 450K - "Best" Normalisation Method?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Scholar 8 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Cufflinks Hangs On
Scholar 8 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Scholar 9 weeks ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference
Popular Question 5 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams
Popular Question 5 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams
Popular Question 6 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 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 Illumina Microarray Annotation
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: how to parallelize single function in R?
Scholar 8 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?
Popular Question 9 months ago, created a question with more than 1,000 views. For Bedgraph And Bigwig Files From Multiple Bams
Popular Question 10 months ago, created a question with more than 1,000 views. For 450K - "Best" Normalisation Method?
Scholar 10 months ago, created an answer that has been accepted. For A: Chrom Sizes for Ensembl Reference

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1826 users visited in the last hour