Moderator: igor

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igor6.8k
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Posts by igor

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Comment: C: Trouble de-multiplexing single index paired-end illumina library
... This was my old protocol for QIIME 1.8. Not sure if it is still valid, but maybe it will give you some ideas. # check fastq header zcat FASTQ/lane1_NoIndex_L001_R1_001.fastq.gz | grep ":N:" | head zcat FASTQ/lane1_NoIndex_L001_R2_001.fastq.gz | grep ":N:" | head # fix barcode r ...
written 2 days ago by igor6.8k
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Comment: C: Trouble de-multiplexing single index paired-end illumina library
... I was using QIIME demultiplexing for paired-end single index, so 3 total reads like in the original post. ...
written 3 days ago by igor6.8k
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Answer: A: BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
... There are actually many different versions of hg38/GRCh38. This post by https://www.biostars.org/u/10932/ describes the human reference genome landscape very nicely: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use Specific discrepancies: - Inclusion of ALT contigs. - Padding AL ...
written 4 days ago by igor6.8k
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Comment: C: Trouble de-multiplexing single index paired-end illumina library
... For some odd reason, it's actually easier to demultiplex with QIIME than try to get QIIME to work with demultiplexed data. The QIIME users I know specifically ask for non-demultiplexed data. At least this was the case with QIIME 1. ...
written 4 days ago by igor6.8k
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Comment: C: How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
... There is now a nice compilation of all the different variations of this question: https://www.biostars.org/p/285757/ ...
written 4 days ago by igor6.8k
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Comment: C: How to know that your RNA-seq is stranded or not?
... There are some great answers posted already, but just in case you want to learn more about strandness, you can also check this previous post: https://www.biostars.org/p/285757/ ...
written 4 days ago by igor6.8k
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Comment: C: Using Bioconductor package for gene expression analysis
... The best thing to do is try to either obtain raw FASTQs (from which the BAMs were generated) or the raw counts (generated from the BAMs). If you are starting with BAMs, you are likely to encounter errors because you will need to obtain a gene annotation file (usually GTF) that is compatible with you ...
written 10 days ago by igor6.8k
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... There are some suggestions in this previous discussion: https://www.biostars.org/p/272889/ You can import the GTF into R as a data frame and then use `dplyr` to filter it. You can also try `plyranges`: https://bioconductor.org/packages/release/bioc/vignettes/plyranges/inst/doc/an-introduction.html ...
written 12 days ago by igor6.8k
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Answer: A: Finding Only Protein Coding Genes from Gencode GTF
... Have you checked [Gene/Transcript Biotypes in GENCODE & Ensembl][1]? There is extensive explanation of the annotation labels there. There is not really a hierarchical structure, so some transcripts could fall into multiple categories (more and less specific). You really have to go through all t ...
written 14 days ago by igor6.8k
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Comment: C: GSEA on single-cell cluster data
... Due to the dropouts, the result for individual cells will be extremely noisy. Cluster-level analysis would be much cleaner. GSEA is not meant for over-representation, but I have seen it used that way many times. Regardless, as I mentioned, there are many other pathway analysis tools that are approp ...
written 14 days ago by igor6.8k

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Teacher 9 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why are there multiple GFP nucleotide sequences?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
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Scholar 3 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data

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