User: T_18

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T_180
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Posts by T_18

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Comment: A: Screening Illumina reads for contamination
... Thanks for your answers, I do not have a reference genome, so this will be de novo. I think therefor that it is beneficial to remove (potential) dodgy reads, and I think removing 200k reads, of 44 million in total will not influence my set a lot. But like to hear your opinion on this. @Friederike, ...
written 10 days ago by T_180 • updated 10 days ago by WouterDeCoster29k
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Screening Illumina reads for contamination
... Dear all, I have a question regarding the screening of contaminants of my Illumina Hiseq reads. My data is RNAseq data and library prep is done using the NEBnext kit. Initially I have cleaned and trimmed the data using trimmomatic, with a specific adapter database . This included trimming the read ...
illumina univec rna-seq written 11 days ago by T_180 • updated 10 days ago by WouterDeCoster29k
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Comment: C: Load fail of GO.db in R
... Ah, of course.. Thanks. But: ulimit -u unlimited -bash: ulimit: max user processes: cannot modify limit: Operation not permitted ...
written 3 months ago by T_180
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Comment: C: Load fail of GO.db in R
... In that case would you argue against setting the stack space to unlimited (like in my reply above)? ...
written 3 months ago by T_180
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Comment: C: Load fail of GO.db in R
... Aha! Thanks.. So no specific R issue here.. Found the following solution: "To improve performance, we can safely set the limit of processes for the super-user root to be unlimited" So therefor added the following line: ulimit -u unlimited using: > sudo nano /root/.bashrc But this resulted in th ...
written 3 months ago by T_180
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Load fail of GO.db in R
... Dear all, I am trying to run GOseq from the bioconductor package in R (via the Trinity pipeline). And get the following error: >Error: package or namespace load failed for ‘GO.db’: .onLoad failed in loadNamespace() for 'GO.db', details: call: NULL error: C stack usage 7969536 is too close ...
R rna-seq written 3 months ago by T_180
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Comment: C: Trimming adapters of Hiseq2000 pair end reads
... Hi all, Sorry for the late response on this topic. In Emma's blastn results I see that the dataset has a blast hit with JX069762.1 and JX069764.1 (perhaps more which I can't see), which are Cloning vectors (pFosill-2 and -4). In my own dataset (insect RNAseq) I have a lot of hits with these cloning ...
written 4 months ago by T_180
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Comment: A: Bulk download of gene names NCBI
... Pierre: you're a (bio)star! Thanks a lot.. ...
written 9 months ago by T_180
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Comment: C: Bulk download of gene names NCBI
... I feel I'm almost there, but bumped into this error: "biostar273687.xsl:73: parser error : Premature end of data in tag stylesheet line 3 cannot parse biostar273687.xsl" Am I correct that there could be an end tag missing? Should there be " on line 5? ...
written 9 months ago by T_180
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Comment: C: Bulk download of gene names NCBI
... I have not found a case where it is only available in the download, the problem is that it is often missing in the download. So the information is available on the gene page (see previous example) but not in the downloaded summary: (Send to> file> summary/ gene feature or any other format): 1 ...
written 9 months ago by T_180

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