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Answer: Can't install hisat2 with miniconda

Answer: iqtree vs raxml

Comment: which statistical test and which package for comapre datasets?

Answer: Bowtie 2 alignment

Answer: GO, KEGG, GSEA analysis with ~5 DEGs

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Comment: Can't install hisat2 with miniconda by Ozymandeus ▴ 30

Thank you! This fixed the issue.

Comment: Tutorials for Spatial Transcriptomics by CTLong ▴ 50

Although I'm not that into ST, but personally, when I learn a new technology, I usually play around with the data that had already been gen…

Comment: Is interleaved Fastq files the same as interlaced fastq by GenoMax 136k

> SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq Both programs will accept separate paired-end files. The reads in the …

Comment: which statistical test and which package for comapre datasets? by LauferVA 3.8k

@414fa591 this question is in need of clarification, as @rpolicastro has already said. However, based on what you've written, ***the resea…

Comment: Bowtie 2 alignment by Elizabeth ▴ 30

Thank you so much. I'm getting comparable results now. Appreciate the quick response.

Comment: which statistical test and which package for comapre datasets? by rpolicastro 12k

You should explain your experiment in more detail, such as the hypothesis you are testing and the samples you have to test this.

Comment: which statistical test and which package for comapre datasets? by satva72 • 0

thanks for you comment. I think its possible if we compare the different dataset?! to show that distribution is different between datasets.

Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra by Jeremy Leipzig 22k

seqr now supports Hail but with a layer of elasticsearch. It does not support TileDB but in theory it could.

Comment: which statistical test and which package for comapre datasets? by Jeremy ▴ 860

I think you will need at least three replicates to be able to do statistics.

Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k

> Asking for bed file is not a suitable option in the current scenario. ???????

Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100

they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…

Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Pierre Lindenbaum 158k

> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....

Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100

thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)

Comment: Is interleaved Fastq files the same as interlaced fastq by rpolicastro 12k

This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…

Comment: Is interleaved Fastq files the same as interlaced fastq by RCMC • 0

Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…

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