User: waqaskhokhar999

Reputation:
10
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
6 years ago
Email:
w**************@gmail.com

about me

Posts by waqaskhokhar999

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
131
views
1
answers
Answer: A: Cut off for DE genes
... log2 fold change can give you better insight of the picture. For more details you can check these links [RNA-Seq workflow for differential gene expression][1] [From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pip ...
written 12 days ago by waqaskhokhar99910
0
votes
1
answer
71
views
1
answers
Comment: C: Bowtie indexes for custom reference genome
... yes we don't need gtf file to build genome index. Good luck ...
written 12 days ago by waqaskhokhar99910
1
vote
1
answer
71
views
1
answers
Answer: A: Bowtie indexes for custom reference genome
... Bowtie can index from a set of DNA sequences. It produces six file which constitute the index. For more details please check this link [manual section on index building][1] [1]: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer ...
written 12 days ago by waqaskhokhar99910
0
votes
2
answers
137
views
2
answers
Comment: C: limitations of Edge R or DEseq
... In case you want to see DE among large number of samples and you don't have replicates you can use EdgeR. Please see the section 2.11 [What to do if you have no replicates][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf ...
written 12 days ago by waqaskhokhar99910
0
votes
2
answers
137
views
2
answers
Answer: A: limitations of Edge R or DEseq
... DESeq is not suitable if you don't have biological replicates but EdgeR can calculate differential gene expression even you don't have biological replicates. ...
written 12 days ago by waqaskhokhar99910
0
votes
1
answer
60
views
1
answers
Comment: C: Trinity for single end library distributed among different lanes.
... I have used SRA_TOOLKIT/fastq-dump to dump the fastq files, since my data is single ended, do i still need to use --split-files as this option is used for paired ended data ...
written 12 days ago by waqaskhokhar99910
0
votes
1
answer
60
views
1
answer
Trinity for single end library distributed among different lanes.
... RNA-seq data is single ended and distributed among different lanes. I am trying to assembel the transcriptome using this command: trinity/trinityrnaseq-Trinity-v2.8.3/Trinity --seqType fq --max_memory 10G --single SRR3460466.fastq,SRR3460467.fastq,SRR3460468.fastq,SRR3460469.fastq,SRR3460470.fa ...
assembly rna-seq written 13 days ago by waqaskhokhar99910 • updated 13 days ago by h.mon21k
0
votes
3
answers
16k
views
3
answers
Comment: C: Pca From Vcf Files
... How can we add label in PCA plot generated by snprelate to see samples? ...
written 21 days ago by waqaskhokhar99910
0
votes
1
answer
1.5k
views
1
answers
Comment: C: SNPRelate: how to give specific color to a population in PCA plot
... How we can label the samples in this PCA plot? ...
written 21 days ago by waqaskhokhar99910
0
votes
3
answers
795
views
3
answers
Answer: A: stringtie and alternative splicing
... DEXseq seems to be a very good option to estimate differential usage of exons but I don't have biological replicates, can I still use DEXseq? ...
written 29 days ago by waqaskhokhar99910

Latest awards to waqaskhokhar999

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1332 users visited in the last hour