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:books: Various bioinformatics tutorials

Home Page: https://hadrieng.github.io/tutorials/

License: Other

education bioinformatics tutorials

tutorials's Introduction

Tutorials

This repository contains basic tutorials and walkthroughs on various bioinformatics subjects:

Dev

First clone the repository and install mkdocs and the theme using pipenv

git clone https://github.com/HadrienG/tutorials.git
cd tutorials
pipenv install

For a live preview in your browser do

pipenv run dev

Deploy

The following command will build and push your website to a gh-pages branch. Only do this if you want your own version of the website! If you are modifying the original, please open a pull request.

pipenv run deploy

tutorials's People

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tutorials's Issues

assign Ensemble gene ids to transcripts

in the RNA seq tutorial in this code block

txdb <- makeTxDbFromGFF("chr22_genes.gtf")
k <- keys(txdb, keytype = "GENEID")
tx2gene <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
head(tx2gene)

GENEID and TXNAME should be swapped

Nanopore tuto: mummer part

The mummer part needs to be changed (ex: no --png option)

Nanopore: mistake in options for wtdbg2

wtdbg2 -x rs -i subset.fasta -fo assembly
-> change to -x ont

"invalid class “phyloseq” object"

Hi! Thanks for make it available! It was running very well for me until this part:

constructing a phyloseq object from our output and newly created metadata

physeq <- phyloseq(otu_table(seq_table_nochim, taxa_are_rows=FALSE),
sample_data(sample_data),
tax_table(taxa),
phy_tree(fitGTR$tree))

I got the follow error message:

error: Error in validObject(.Object) : invalid class “phyloseq” object:
Component sample names do not match.
Try sample_names()
Calls: phyloseq ... do.call -> new -> initialize -> initialize -> validObject
Execution halted

Could you help me ?

Dependabot can't resolve your Python dependency files

Dependabot can't resolve your Python dependency files.

As a result, Dependabot couldn't update your dependencies.

The error Dependabot encountered was:

ERROR: ERROR: Could not find a version that matches markdown>=2.3.1,>=3.2
Tried: 1.7, 1.7, 2.0, 2.0, 2.0.1, 2.0.1, 2.0.2, 2.0.2, 2.0.3, 2.0.3, 2.1.0, 2.1.0, 2.1.1, 2.1.1, 2.2.0, 2.2.0, 2.2.1, 2.2.1, 2.3, 2.3, 2.3.1, 2.3.1, 2.4, 2.4, 2.4.1, 2.4.1, 2.5, 2.5, 2.5.1, 2.5.1, 2.5.2, 2.5.2, 2.6, 2.6, 2.6.1, 2.6.1, 2.6.2, 2.6.2, 2.6.2, 2.6.3, 2.6.3, 2.6.4, 2.6.4, 2.6.5, 2.6.5, 2.6.6, 2.6.6, 2.6.7, 2.6.7, 2.6.8, 2.6.9, 2.6.10, 2.6.11, 2.6.11, 3.0, 3.0, 3.0.1, 3.0.1, 3.1, 3.1, 3.1.1, 3.1.1
There are incompatible versions in the resolved dependencies.
[pipenv.exceptions.ResolutionFailure]:       req_dir=requirements_dir
[pipenv.exceptions.ResolutionFailure]:   File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 726, in resolve_deps
[pipenv.exceptions.ResolutionFailure]:       req_dir=req_dir,
[pipenv.exceptions.ResolutionFailure]:   File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 480, in actually_resolve_deps
[pipenv.exceptions.ResolutionFailure]:       resolved_tree = resolver.resolve()
[pipenv.exceptions.ResolutionFailure]:   File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 395, in resolve
[pipenv.exceptions.ResolutionFailure]:       raise ResolutionFailure(message=str(e))
[pipenv.exceptions.ResolutionFailure]:       ResolutionFailure: ERROR: ERROR: Could not find a version that matches markdown>=2.3.1,>=3.2
[pipenv.exceptions.ResolutionFailure]:       Tried: 1.7, 1.7, 2.0, 2.0, 2.0.1, 2.0.1, 2.0.2, 2.0.2, 2.0.3, 2.0.3, 2.1.0, 2.1.0, 2.1.1, 2.1.1, 2.2.0, 2.2.0, 2.2.1, 2.2.1, 2.3, 2.3, 2.3.1, 2.3.1, 2.4, 2.4, 2.4.1, 2.4.1, 2.5, 2.5, 2.5.1, 2.5.1, 2.5.2, 2.5.2, 2.6, 2.6, 2.6.1, 2.6.1, 2.6.2, 2.6.2, 2.6.2, 2.6.3, 2.6.3, 2.6.4, 2.6.4, 2.6.5, 2.6.5, 2.6.6, 2.6.6, 2.6.7, 2.6.7, 2.6.8, 2.6.9, 2.6.10, 2.6.11, 2.6.11, 3.0, 3.0, 3.0.1, 3.0.1, 3.1, 3.1, 3.1.1, 3.1.1
[pipenv.exceptions.ResolutionFailure]: Warning: Your dependencies could not be resolved. You likely have a mismatch in your sub-dependencies.
  First try clearing your dependency cache with $ pipenv lock --clear, then try the original command again.
 Alternatively, you can use $ pipenv install --skip-lock to bypass this mechanism, then run $ pipenv graph to inspect the situation.
  Hint: try $ pipenv lock --pre if it is a pre-release dependency.
ERROR: ERROR: Could not find a version that matches markdown>=2.3.1,>=3.2
Tried: 1.7, 1.7, 2.0, 2.0, 2.0.1, 2.0.1, 2.0.2, 2.0.2, 2.0.3, 2.0.3, 2.1.0, 2.1.0, 2.1.1, 2.1.1, 2.2.0, 2.2.0, 2.2.1, 2.2.1, 2.3, 2.3, 2.3.1, 2.3.1, 2.4, 2.4, 2.4.1, 2.4.1, 2.5, 2.5, 2.5.1, 2.5.1, 2.5.2, 2.5.2, 2.6, 2.6, 2.6.1, 2.6.1, 2.6.2, 2.6.2, 2.6.2, 2.6.3, 2.6.3, 2.6.4, 2.6.4, 2.6.5, 2.6.5, 2.6.6, 2.6.6, 2.6.7, 2.6.7, 2.6.8, 2.6.9, 2.6.10, 2.6.11, 2.6.11, 3.0, 3.0, 3.0.1, 3.0.1, 3.1, 3.1, 3.1.1, 3.1.1
There are incompatible versions in the resolved dependencies.

['Traceback (most recent call last):\n', '  File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 501, in create_spinner\n    yield sp\n', '  File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 649, in venv_resolve_deps\n    c = resolve(cmd, sp)\n', '  File "/usr/local/.pyenv/versions/2.7.17/lib/python2.7/site-packages/pipenv/utils.py", line 539, in resolve\n    sys.exit(c.return_code)\n', 'SystemExit: 1\n']

If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.

View the update logs.

update assembly tuto

We need to update the Busco part to quast -b instead (with dl of the bacterial db, file renaming of the tar.gz).
Maybe we could add a part in the beginning with all the conda install needed

Bowtie2 mapping command update

In the Aligning Reads section , the command is listed as:

bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq.gz \
    -2 SRR957824_trimmed_R2.fastq.gz -S SRR957824.sam

However, .gz compressed files were not generated in the previous sections, just flat SRR957824_trimmed_R1.fastq and SRR957824_trimmed_R2.fastq files. So either those files should be gz compressed or the command here updated to :

bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq \
    -2 SRR957824_trimmed_R2.fastq -S SRR957824.sam

Is it GFF or GTF | We can use our .gtf annotation for that, and the GenomicFeatures package: txdb <- makeTxDbFromGFF("chr22_genes.gtf")

Hello,

You state (https://www.hadriengourle.com/tutorials/rna/#downloading-the-data):

"We can use our .gtf annotation for that, and the GenomicFeatures package:

txdb <- makeTxDbFromGFF("chr22_genes.gtf")"

Yet when I run this with a gtf file, I get "Import genomic features from the file as a GRanges object ... Error in readGFF(filepath, version = version, columns = columns, tags = tags, :
reading GFF file: line 1 has more than 9 tab-separated columns"

Obviously these are two different files formats, did you mean you need to use a GFF file because there doesn't seem to be a GTF version of the above function i.e. makeTxDbFromGTF?