User: maria.traka

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maria.traka20
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2 years, 3 months ago
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m**********@quadram.ac.uk

Posts by maria.traka

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Adding gene names to ballgown object gexpr(bg)
... I'm using the Ensembl Homo_sapiens.GRCh38.89.gtf dowloaded from their ftp site so it's not that. I suspect these are putative novel isoforms of known genes that are listed and because they happened to be listed before the known transcripts match is hitting those. I have now managed a workaround wher ...
written 23 months ago by maria.traka20
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Adding gene names to ballgown object gexpr(bg)
... Hi, I'm having an issue with adding names to the gene expression of a bg object. It seems that the texpr$gene_id has multiple entries for the same MSTRGx (as expected I guess considering it's different isoforms for the same gene) but unfortunately for some of the genes the first one of the texpr ent ...
ballgown rna-seq written 23 months ago by maria.traka20
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Answer: A: cutadapt error while performing Trim_Galore
... Update: Thanks to all your help above I now have a good idea of where the errors are. Thanks! After a bit more digging it seems that the latest sortmerna (v2.1) that generated these files has a bug that introduces errors. Until this is fixed the suggestion is to increase the memory allocation. I am ...
written 2.3 years ago by maria.traka20
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Comment: C: cutadapt error while performing Trim_Galore
... I get: 175654078 LIB27930_non_rRNA_unmerged1.fastq ...
written 2.3 years ago by maria.traka20
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Comment: C: cutadapt error while performing Trim_Galore
... head -n 1 LIB27930_non_rRNA_unmerged1.fastq | sed -n 'l' @HISEQ:171:CAUJ2ANXX:8:1101:1212:2104 1:N:0:TGTATCGGCCGG$ This is what i get if i look at line 1... ...
written 2.3 years ago by maria.traka20
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cutadapt error while performing Trim_Galore
... Hi, I've been trying to run trim_galore for 115 libraries and although 109 of them work perfectly for 7 of them i get the following message that Line 1 does not start with a @, which it does! I have gone back to the previous step and regenerated the file but still get the same error message. Can yo ...
trim_galore cutadapt written 2.3 years ago by maria.traka20

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