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Answer: SNP calling from multiple genomes: No valid SNPs
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colindaven
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The typical SNP calling route is to run say 3 short read datasets (fastq input) against one reference genome. Then your approach would like…
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https://bioconductor.org/books/3.15/OSCA.intro/index.html is a comprehensive version of scRNAseq analysis. Installation of software would b…
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Usage section for the pipeline: https://nf-co.re/pairgenomealign/2.1.0/docs/usage/
You need to specify a "target" genome using the paramet…
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I finally got access to a more powerful machine, but this time I got the error:
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$ ~/src/Nextflow/nextflow run nf-core/pairgenomealign …
Answer: HOMER findMotifsGenome.pl failed compilation
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I use the commamd `conda install perl==5.32.1 ` solve this problem
Comment: normalize between 2 different platform
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linqy
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Hello,
Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? T…
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
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gynecoloji
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Thanks for your response.
I think it may be better to keep those repetitive regions and only filter out the blacklisted regions.
This is a …
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
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jared.andrews07
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IDR addresses a different problem than removal of reads aligning to blacklist reads, though it's unquestionably useful for deriving more ro…
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Simply posting a snippet of error message in a question is the reason you have not received any responses.
Please make an effort to formu…
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Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583
I believe I just needed to place the "build" c…
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ATS
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That's great to know. Thanks for your input!
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
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It should be noted that concerns about mapping artifacts in ChIP-seq really come from an era where reads were 36bp (or even 25bp!) in lengt…
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LChart
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AGain you seem to be over-filtering. Your mean.k and median.k are really low, so I think the number of input genes you used for this is ver…
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
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I am going to guess you've seen/thoroughly read [this paper about the ENCODE blacklist regions](https://www.nature.com/articles/s41598-019-…
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