Top new questions this week:
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I am able to find matching motifs on a single sequence, as well as their position as shown below : …
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Similar to: How to convert data in gmt format to dataframe? I have downloaded a GMT file from the GSEA database (www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022….
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I have pairwise distance data for single linkage cluster and I would like to convert it to newick format. I was unable to find a conversion algorithm. I require newick format for visualization and …
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Do you think it’s possible to combine short read Illumina libraries (WGS) from multiple closely related eukaryotic microbial strains (e.g. libraries from a re-sequencing study, >99% ITS1 sequence) …
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What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake we processed some samples with poor quality RNA to generate long read. Now we are …
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I want to compare the headers from the fasta file to file1, and if there’s a match, reorganize the header and put the match first. If there’s no match between fasta file and file1, look at file2 and …
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I am seeking statistical support for the following bacterial growth time series. In the lab, we have cell cultures growing in bioreactors. Every day we measure the concentration in mmol-1 of a set of …
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Greatest hits from previous weeks:
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I’m currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups …
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As enrichment analysis a usual step is to infer the pathways enriched in a list of genes. However I can’t find a discussion about which database is better. Two of the most popular (in my particular …
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What are the pros and cons of the different basecallers in Oxford Nanopore Technology Sequencing? I am about to start a MinION run on my laptop. What should I consider when choosing my basecaller? …
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I apologize for this very basic question. With @Michael G.’s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and …
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Well, I’m trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart. I tried to get a kind of conversion table for all human genes. …
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I would like to convert a BED format to GFF3. The only useful tool that I could find via a google search seems to be Galaxy, …
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I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
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