User: geneticatt

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geneticatt20
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Posts by geneticatt

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Adding in a specific place to a file in python
... Ok, you can can use an enumerated loop through the lines to save that index to a variable for use in the above indexing step. for e, line in enumerate(lines): if line.strip() == ";": idx = e break .strip() method will get rid of any whitespace that might mess w ...
written 8 weeks ago by geneticatt20
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Answer: A: Adding in a specific place to a file in python
... You can read the file and save the lines above your breakpoint as one variable and the lines below as another variable. with open("nex.nexus", "a") as myfile: lines = myfile.readlines() top = lines[:7] bottom = lines[7:] You can then adjust the writing steps acco ...
written 8 weeks ago by geneticatt20
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Comment: C: What would be the best strategy to merge the GO annotation from blast2go, InterP
... It depends on what you mean by "pool the results". Would you like to produce a table that includes that annotation from each of these tools for each transcript? If so, you might want to try EnTAP, which is a new transcriptome annotation tool that wraps all of the tools you mentioned in your question ...
written 9 weeks ago by geneticatt20
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Comment: C: freebayes SNP calling question
... It seems like you'e missing the sequence `TA_12g0050` in your fasta. Freebayes will index the file for you if it doesn't already exist. Are you using a full genome assembly or a set of gene models as the reference? You should compare the ID list from the fasta file and reference IDs from the bam to ...
written 9 weeks ago by geneticatt20
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Comment: C: Using Trinity for DGE - how to input study design
... I guess that your controls will be a non-injured specimens from different treatments. This question doesn't seem very relevant to the Trinity de-novo assembler, instead this inform the strategy of downstream analysis and potentially the construction of a combined reference which is built from the li ...
written 9 weeks ago by geneticatt20
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Comment: C: Plant orthologous genes
... @genomax, It looks like the last update to this database was in 2015. Finding orthologs manually is a much better option as many of the genomes of interest here have gone through multiple assembly and annotation iterations and several have complete genomes from multiple cultivars. For example, [a fu ...
written 9 weeks ago by geneticatt20
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Answer: A: gene length for calculating TPM values
... Here the width column includes any existing introns, so you can't use the width from this particular table to calculate TPM. The gencode.v33.annotation.gtf likely has the intron ranges, which you can use for your calculation. ...
written 9 weeks ago by geneticatt20
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Answer: A: Plant orthologous genes
... The way that I've handled this issue in the past is by downloading the amino acid sequences for each species of interest from their respective databases and using [OrthoFinder's][1] phylogenetic orthology inference tool. The sequences will cluster into groups of orthologs and paralogs. [1]: http ...
written 9 weeks ago by geneticatt20
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Comment: C: Converting VCF to CSV file
... Is there a particular danger in using something like sed for this? sed 's/\t/,/g' input.vcf > output.vcf ...
written 9 weeks ago by geneticatt20
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Comment: A: HISAT2 alignment problem
... I'm getting the same error when running hisat2 (also as a batch submission script). I don't have permissions to edit the script on our cluster. For the case that it does need to be fixed, is there a way to copy the script and provide its location in the batch script so that hisat is provided the alt ...
written 5 months ago by geneticatt20

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