User: Raito92

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Raito9240
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New User
Location:
Italy
Last seen:
2 weeks, 3 days ago
Joined:
1 month, 3 weeks ago
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t***************@gmail.com

Posts by Raito92

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Function kegga not working for species other than the conventional ones - Pathwa
... Hello, first of all, thanks for your kind and detailed answer! Yes, you guessed it right, I used the domestic olive tree genomic annotation from the Spanish team you mentioned! I realised later that there is, indeed, a way to relate such genes to the wild olive tree ones, and it is contained in th ...
written 19 days ago by Raito9240
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Comment: C: Function kegga not working for species other than the conventional ones - Pathwa
... Hi, thanks for your answer! Yes, I realised later that the answer could be using the NCBI codes of the genome mine was annotated on (wild olive tree, while mine is the domestic olive tree) ... so it looks as if all I need is to merge some data to obtain the NCBI codes before, and then pass such new ...
written 19 days ago by Raito9240
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Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
... Hi! I'm running the function 'kegga' to perform a pathyway analysis on my olive tree data (a species for which a default package doesn't exist), but I get this error... ![enter image description here][1] I think the problem may be my Gene names, which aren't normal NCBI Gene IDs... https://i.ibb. ...
limma kegg pathway analysis kegga written 23 days ago by Raito9240 • updated 20 days ago by Gordon Smyth37k
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Comment: C: Improving the performance of the align function from Rsubread for old Roche454 r
... Thanks for your answer! ...
written 23 days ago by Raito9240
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Comment: C: Improving the performance of the align function from Rsubread for old Roche454 r
... I thought over it better. The genome is complete, at least in its coding parts, which are the ones used for RNA reads alignment. So, having an incomplete reference in non-coding areas shouldn't really affect the result... Instead, the great heterozigosity of the genome of the organism I'm working on ...
written 4 weeks ago by Raito9240
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Comment: C: Improving the performance of the align function from Rsubread for old Roche454 r
... Hello, thanks for your answer and suggestion! Even by setting a higher mismatch threshold (7 instead of the default 3) and editing the length read to an ever larger tolerance range (the latter making no difference at all), I was only able to obtain an average 64% of mapped reads rather than the orig ...
written 5 weeks ago by Raito9240
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Comment: C: No method for coercing this S4 class to a vector, as trying to import my own dat
... I solved the problem! ...
written 5 weeks ago by Raito9240
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Improving the performance of the align function from Rsubread for old Roche454 reads
... Hello again! I'm running a RNASeq analysis with some old, unpublished Roche454 data, using the workflow RnaSeqGeneEdgeRQL. However, reads from Roche454 aren't the best for this kind of analysis, being longer than Illumina ones and the method itself is quite outdated. So, in my opinion, it's likely t ...
rnaseq rsubread align roche454 written 5 weeks ago by Raito9240 • updated 27 days ago by Wei Shi3.1k
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How to add my own Entrez Gene IDs rather than using the ones from a default package?
... Hello! I'm using the workflow RnaSeqGeneEdgeRQL to analyse some RNASeq data, and I've by now arrived to the end of my analysis, missing only the pathway analysis to contextualize genes with different expression levels. The workflow itself is studied for mouse genes, and suggests, at a point, to imp ...
annotation software error gene entrez ids written 5 weeks ago by Raito9240 • updated 5 weeks ago by Gordon Smyth37k
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Comment: C: No method for coercing this S4 class to a vector, as trying to import my own dat
... Solved, I just had to pass the fastqPath rather than the reads object. XD Sorry. ...
written 6 weeks ago by Raito9240

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