MultiQC
pyrodigal
| MultiQC | pyrodigal | |
|---|---|---|
| 5 | 1 | |
| 1,173 | 122 | |
| 1.5% | - | |
| 9.7 | 8.7 | |
| 4 days ago | 18 days ago | |
| JavaScript | Cython | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
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MultiQC
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R pipelines for bulk RNA-seq analyses
fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
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RNA-seq analysis
I would recommend looking at the pages for FastQC and MultiQC. I run FastQC on my fastq files, then MultiQC on them to collect all that individual data into one report. You can also use MultiQC to analyze the quality of your alignments, at least after using STAR aligner (probably others too, I just have only used STAR aligned).
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How to use MultiQC? I am trying to run it to compile the summary from my FASTQC but I keep getting the "Sample has no read" error.
If that all checks out then I would have to see more of your files in order to help, sorry. Submitting the issue at https://github.com/ewels/MultiQC/issues would help you more
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How can I keep Docker MultiQC from ignoring my large files?
I have seen this Github thread, but it is not applicable for me because I am not running MultiQC natively, I am running a docker version of it in HPC.
pyrodigal
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DNA to amino acid sequence?
True! I believe bakta relies on this python implementation of prodigal for translation https://github.com/althonos/pyrodigal
What are some alternatives?
finviz - Unofficial API for finviz.com
Prodigal - Prodigal Gene Prediction Software
Sooty - The SOC Analysts all-in-one CLI tool to automate and speed up workflow.
cyvcf2 - cython + htslib == fast VCF and BCF processing
awesome-single-cell - Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
orfipy - Fast and flexible ORF finder
tm_calculator_gui - Calculates the melting temperature(in Celsius) of a user imported forward and reverse primer based on primer blast default parameters & pcr additives
DNA-to-Protein-sequence - Translate a string containing a nucleotide sequence(DNA) into a string containing the corresponding sequence of amino acids.
Osintgram - Osintgram is a OSINT tool on Instagram. It offers an interactive shell to perform analysis on Instagram account of any users by its nickname
pybase64 - Fast Base64 encoding/decoding in Python
Sniffles - Structural variation caller using third generation sequencing
DNA-to-Amino-Acid-Converter - This program breaks apart a DNA string and dispalys each amino acid associated with each codon