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User: waqaskhokhar999

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Posts by waqaskhokhar999

<prev • 17 results • page 1 of 2 • next >
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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 9 weeks ago by waqaskhokhar999 • 10
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Comment: C: Bowtie indexes for custom reference genome
... yes we don't need gtf file to build genome index. Good luck ...
written 9 weeks ago by waqaskhokhar999 • 10
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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 9 weeks ago by waqaskhokhar999 • 10
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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 9 weeks ago by waqaskhokhar999 • 10
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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 9 weeks ago by waqaskhokhar999 • 10
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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 9 weeks ago by waqaskhokhar999 • 10
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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 10 weeks ago by waqaskhokhar999 • 10 • updated 10 weeks ago by h.mon ♦ 22k
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Comment: C: Pca From Vcf Files
... How can we add label in PCA plot generated by snprelate to see samples? ...
written 11 weeks ago by waqaskhokhar999 • 10
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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 11 weeks ago by waqaskhokhar999 • 10
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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 12 weeks ago by waqaskhokhar999 • 10

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