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How can I programmatically obtain ftp links to RNA seq fastq files in ENA? Here's an example of a link that I would be interested in obtaining: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR824/000/SRR8240860/SRR8240860_1.fastq.gz In particular,...
Asked on 08/22/2021
3 answerI need to calculate Isoelectric point from a multifasta file, is there any python code or web tool that allows me to do that?...
Asked on 08/22/2021 by farinelli
1 answerI have bacterial chromosomes/plasmids that I have downloaded off refseq in a multi-fasta that I would like to fragment into non-overlapping fragments of between 1 kb and 15 kb. I...
Asked on 08/22/2021 by Stanley Ho
2 answerA collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to use this data in phyloseq, however,...
Asked on 08/22/2021 by Reebola95
0 answerAssume that I have three different Affymetrix microarray experiments, 2x U133 (from 2015 and 2017) and 1xU133 Plus 2.0 (2019). Each array contains several different samples, some of them are...
Asked on 08/22/2021 by Adamm
0 answerI installed gzip package in Conda environment, then to make sure the software was there, I used "ls" command, it was not in the list. Tried to install again,...
Asked on 08/22/2021 by user9196
1 answerI am working with virus nanopore sequencing data. I have to remove host genome from the reads. I want to run the QC on the fastq file after host genome...
Asked on 08/22/2021 by Arun Venugopalan
0 answerI found this documentation on pyOpenMS mass spec library. I want to try different peak picking algorithms. Unfortunately, the docs are not very detailed and don't show...
Asked on 08/22/2021
2 answerI am using OrthoFinder to find orthogroups between species. I am using the latest version unpacked through tar as per their instructions. Orthofinder creates an output folder according to the...
Asked on 08/22/2021 by Michael Winter
1 answerI'm new to Python/Biopython programming. I'd like to install Biopython into my PyCharm IDE but I've tried all instructions on this, but it's not confirming it. I have the available...
Asked on 08/22/2021 by BioIsaac
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