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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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Answer: Tutorials for Spatial Transcriptomics by CTLong ▴ 50

Personally, when I learn a new technology, I usually play around with the data that had already been generated by previous labs and try to …

Comment: What apps can read large FASTQ files on Windows? by ATpoint 78k

Also, as I suggested already here https://bioinformatics.stackexchange.com/questions/21931/how-to-download-sequencing-data-on-windows-using…

Answer: What apps can read large FASTQ files on Windows? by size_t ▴ 120

As @Sanjukta said, you won't really learn anything new from manually looking at millions of sequences. If you insist on viewing, you c…

Comment: What apps can read large FASTQ files on Windows? by dsull ★ 5.1k

Why do you want to open up such a large file in a text editor? You're not really going to learn anything new from manually looking at milli…

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

Thank you! This fixed the issue.

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....

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