User: Cristina Zamora

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Posts by Cristina Zamora

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Job: THREE postdoctoral positions in Molecular Biology and Bioinformatics in UVa (SPAIN)
... We are hiring three enthusiastic, thorough and collaborative postdocs to join the Forest Pathology Group at Universidad de Valladolid (Campus of Palencia, Spain). The lab has two ongoing projects, the positions will be shared as follows: (i) **1 post-doctoral position for 1 year** is available in t ...
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Comment: A: Comparison of comparisons with edgeR
... Thank you both!!! :) I have opted of following the 3.3.4 section of edgeR manual with the design: species_design <- model.matrix(~species+exposure+species:exposure, data=targets) Assuming Inoculated versus Control in Resistant species as baseline. (Intercept) speciesS exposureInocu ...
written 11 weeks ago by Cristina Zamora0 • updated 11 weeks ago by GenoMax95k
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Comparison of comparisons with edgeR
... Suppose you have four experimental conditions for your RNA-seq: -Resistant species inoculated by a pathogen, -Resistant species control, -Susceptible species inoculated by a pathogen, -Suceptible species control, each with three replicates. Your RNA-seq samples look like the following: R1 ...
gene expression rna-seq edger written 11 weeks ago by Cristina Zamora0 • updated 11 weeks ago by GenoMax95k
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Comment: C: gffread error when extracting transcript sequences from gtf, coordinates exceed
... It is already fixed, my gtf had an awful 2-line header that I had to remove. Now it is working perfectly, thank you for your script! ...
written 5 months ago by Cristina Zamora0
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Comment: C: How to extract fasta sequences from assembled transcripts generated by Stringtie
... There is a Python script that fixes this error, you can follow https://www.biostars.org/p/264727/#264892 ...
written 5 months ago by Cristina Zamora0
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Comment: C: gffread error when extracting transcript sequences from gtf, coordinates exceed
... Dear Victor I'm using your pyton script to fix my gtf but I got the following error: Traceback (most recent call last): File "/home/uva_dpvrf_1/uva_dpvrf_1_1/bin/gtf_fixer_to_gffread.py", line 23, in transcript_end = int(line_list[4]) IndexError: list index out of range I have no idea how to ...
written 5 months ago by Cristina Zamora0
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Comment: C: Retrieving GO mappings for GOseq analysis with non-native organism
... Thank you. Finally I had to modify all the document with BASH and R forcing it to look like "GENEID" "ONTOLOGY" "GOID" "TERM" PITA_XXXXX CC GO:XXXXX cellular_component Individual GO terms in each row for all the genes. By the way, annotation1000$Query_sequence was my mistake. ...
written 7 months ago by Cristina Zamora0
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Comment: C: Example of gene2cat goseq
... Thanks for your advice. Could you provide a link to follow the script of the Trinity website? I need to generate the list of lists you mentioned and I can't find it. Thank you! ...
written 7 months ago by Cristina Zamora0
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Comment: C: Retrieving GO mappings for GOseq analysis with non-native organism
... Thank you for the help, I'm going through the same problem. What I can't understand is how the gene2cat file should look. In my case, I have a table with the gene ids and the GO terms divided by category (GO_Biological, Go_Cellular, etc) (see picture at bottom). I have done a try using GO_Biological ...
written 7 months ago by Cristina Zamora0 • updated 7 months ago by i.sudbery10k

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Supporter 11 weeks ago, voted at least 25 times.

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