User: s_herrera

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s_herrera10
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10 months, 1 week ago
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Posts by s_herrera

<prev • 7 results • page 1 of 1 • next >
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How to draw a Synteny map from coordinates file
... Hello, I want to draw a Synteny map between a chromosome-level genome (reference) and a draft genome which is not assembled to chromosome level. I already have the output of SatsumaSynteny (satsuma_synteny.refined.out), which has the coordinates of the syntenic blocks, and looks like this: chrX ...
synteny map satsuma synteny written 10 months ago by s_herrera10
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PROVEAN input script
... Hi everyone, I would like to write a python script to extract amino acid substitutions and indels from several protein alignments, and use it as an input for variant effect prediction with PROVEAN. So far I have modified an initial script (https://www.biostars.org/p/258130/#259863) to extract only ...
python provean variant effect prediction written 2.9 years ago by s_herrera10
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Comment: C: How to extract polymorphic positions from several alignments?
... Hi @Rodrigo, Thank you very much! This is incredibly useful. I just had to added `.decode('UTF-8')` when concatenating `main_letter` and `letter` as follows: `change = main_letter.decode('UTF-8') + str(column + 1) + letter.decode('UTF-8')`, because otherwise the script returns this error message: ...
written 3.1 years ago by s_herrera10
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Comment: C: FPKM values from SE vs. PE RNA-Seq libraries
... Thanks @genomax, however I'm using fpkm values for both single-end and paired-end libraries, and I don't understand why there are such great differences in fpkm values. ...
written 3.1 years ago by s_herrera10
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FPKM values from SE vs. PE RNA-Seq libraries
... Hi everyone, I have a question regarding the use of RSEM for estimating isoform expression levels from RNA-Seq data. I have 5 different RNA-Seq assemblies (**4 are SE and the remaining one is PE**) from different species of the same tissue. The species are divided in two groups (A and B) and I'm i ...
gene fpkm differential-expression rna-seq written 3.1 years ago by s_herrera10 • updated 23 months ago by Biostar ♦♦ 20
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How to extract polymorphic positions from several alignments?
... Hi everyone, I have several fasta protein alignments (~5000) and I would want to identify polymorphic positions plus the aminoacid residues that change between sequences. I have tried to write a code myself, but it has been very difficult (I'm new in programming), and I looked on BioPython but I ha ...
python alignment snp written 3.1 years ago by s_herrera10 • updated 3.1 years ago by Rodrigo150
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How to track which protein ID is linked to which gene ID with rentrez
... I have a bunch of protein IDs and I want to fetch the corresponding coding sequences (CDSs) without loosing the protein ID. I have managed to download the corresponding CDSs, but unfortunately, CDSs IDs are very different from protein IDs in NCBI. I have the following R code: library(rentrez) ...
ncbi R rentrez written 3.2 years ago by s_herrera10

Latest awards to s_herrera

Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to extract polymorphic positions from several alignments?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For PROVEAN input script
Popular Question 2.4 years ago, created a question with more than 1,000 views. For FPKM values from SE vs. PE RNA-Seq libraries

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