User: Abiterkuile

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Abiterkuile20
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Posts by Abiterkuile

<prev • 13 results • page 1 of 2 • next >
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Comment: C: NM_transcript ID gene identification
... Got it working in the end.Thank you very much for all your help. This is contributing towards data analysis for my BSc dissertation. Would you like to give me your credentials so your help can be acknowledged in my dissertation? ...
written 6 months ago by Abiterkuile20
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Comment: C: NM_transcript ID gene identification
... I have formatted all of my IDs into a file like this (one ID per line) >XM_017006279.1 ...
written 6 months ago by Abiterkuile20
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Comment: C: NM_transcript ID gene identification
... Hi thanks for getting back to me. I'm having issues still. Here is the error with one ID (the same error occurs repeatedly when I include my query ID file in foor loop). It seems to want an index file because -i is the option for index. No idea what's going wrong. efetch -db nuccore -id NM_021088 ...
written 6 months ago by Abiterkuile20
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Comment: C: NM_transcript ID gene identification
... Hi there, due to an error i've realised i actually have to do this for around 300 transcripts IDs. Im trying to use your command in linux but struggling to understand how you did this. Is nuccore a file you could share with me please? ...
written 6 months ago by Abiterkuile20
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Comment: C: NM_transcript ID gene identification
... Hi there, due to an error i've realised i actually have to do this for around 300 transcripts IDs. Im trying to use your command in linux but struggling to understand how you did this. Is nuccore a file you could share with me please? ...
written 6 months ago by Abiterkuile20
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Comment: C: NM_transcript ID gene identification
... Great thank you very very much! Much appreciated ...
written 6 months ago by Abiterkuile20
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NM_transcript ID gene identification
... I have 76 differentially expressed Refseq human transcript IDs (mostly NM transcript IDs but some are also XM). I wanted to identify the gene names related to the transcripts using DAVID however it doesn't seem to recognise NM or XM transcript IDs. I used panther and it identified 36, however 39 ...
refseq panther gene ontology david rna-seq written 6 months ago by Abiterkuile20 • updated 6 months ago by genomax55k
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Comment: C: Sleuth_prep error in R - unused argument
... session info in R R version 3.4.3 (2017-11-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.125 ...
written 6 months ago by Abiterkuile20
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Sleuth_prep error in R - unused argument
... Hi there, I'm new to Sleuth and R. I've been experiencing an error in sleuth during sleuth_prep and struggling to understand it. > so <- sleuth_prep(s2c, ~ condition) reading in kallisto results dropping unused factor levels ............................. Error in `[.data.table`(counts_test, ...
software error R sleuth kallisto rna-seq written 6 months ago by Abiterkuile20
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add gene names from RefSeq instead of ENSEMBL using biomaRT for sleuth when reading kallisto output
... Hi there, I have reads that have been aligned using Kallisto constructed with a Refseq reference transcriptome (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_rna.fna.gz). In order to include gene names into transcript-level analysis in Sleuth ...
sleuth alignment refseq biomart rna-seq written 6 months ago by Abiterkuile20 • updated 6 months ago by Emily_Ensembl15k

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