Moderator: igor
igor ♦ 6.8k
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Posts by igor
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... 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
igor ♦ 6.8k
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... I was using QIIME demultiplexing for paired-end single index, so 3 total reads like in the original post. ...
written 3 days ago by
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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... 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
igor ♦ 6.8k
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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
igor ♦ 6.8k
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