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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 12 days 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 12 days 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 12 days 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 12 days 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 12 days 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 12 days 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 13 days ago by waqaskhokhar999 • 10 • updated 13 days ago by h.mon ♦ 21k
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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 21 days 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 21 days 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 29 days ago by waqaskhokhar999 • 10

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