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Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
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hmmsearch vs hmmscan - e-value, speed, & output differences?
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Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
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> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `,
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
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Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
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> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
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GenoMax
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While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
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Giulia
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The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
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Assa Yeroslaviz
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and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
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No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
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If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list
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Assa Yeroslaviz
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I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
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Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ? >The database can also be accessed via the API. The same API points …
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Anitha
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Thank you for the information.
Comment: LncRNA Nomenclature
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My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
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ATpoint
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At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
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Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
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RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
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