Top new questions this week:
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From the bedtools intersect man (for version 2.30.0):
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I have a csv file which describes number of chunks per chromosome, like;
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How should I do:
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if ($(params.aligner) == "bowtie") {
align_bowtie2(get_fq_info.out.fq_info)
}
else {
align_bwa(get_fq_info.out.fq_info)
}
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I am experiencing timeout problems when downloading the NCBI nr preformatted blast database using the update_blastdb script (version 504861).
I run the script with the following paramters
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I have set of ~5 processes which perform very similar tasks such that their differences can be parameterized. Rather than putting 5 items through some channel (which seems complicated), or defining 5 ...
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Greatest hits from previous weeks:
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When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download?
You have a combination of choices.
First part options:
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I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 ...
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What the difference between TPM and CPM when dealing with RNA seq data?
What metrics would you use if you have to perform some down stream analysis other than Differential expression for eg.
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I'm very new to bioinformatics in general, and I'm trying to understand some basic concepts.
I have RNAseq data, and bioinformatics people tell me that intensities cannot be compared across patients. ...
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In this answer, it is stated that ribosomal genes should be excluded prior to normalization in scRNA-seq as contaminants.
Do mitochondrial genes have to be excluded as well? I plotted the top 50 ...
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I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...
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Is there a convenient way to extract the longest isoforms from a transcriptome fasta file? I had found some scripts on biostars but none are functional and I'm having difficulty getting them to work.
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