thomas duge de bernonville
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2 answers
1 votes
135 views
How to tell if library generation for RNA-seq experiments are stranded vs not stranded
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3 votes

If you already have a reference transcriptome assembly, then you may run the Salmon tool for quantification using your RNA-seq samples. It has an automated library type inference function (https://...

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4 answers
3 votes
467 views
Comparing phylogeny in R
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3 votes

phangorn is a really powerful package for phylogenies. But to compare the trees, I think you may convert them into dendrograms and calculate a correlation measure, such as the Fowlkes-Mallows Index or ...

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1 answers
1 votes
3k views
local BLAST error: BLAST Database error: Error: Not a valid version 4 database
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2 votes

first I recommend you to check your downloaded data with md5 to be sure there was no problem with that step. How many files did you download? Also I was curious if you had another BLAST+ version ...

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3 answers
1 votes
154 views
How can I obtain FTP links to studies in ENA?
2 votes

Here are some command lines I used for that purpose in bash. Simply prepare a text file containing each accession number (SRR/ERR) you want and create a for loop. Here I used prozilla to speed up ...

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1 answers
0 votes
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Mapping UniProt id to Entrez id
2 votes

The Retrieve/ID mapping tool from Uniprot allows you to convert from Uniprot to entrez ID and vice-versa. It is available here. Just select the appropriate values in the 2.Selection options panel.

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3 answers
2 votes
180 views
FASTQ file trimming
2 votes

If you need the quality vector for each read, then your code will create a shift because it does not cut the quality vector. You should rather use a trimming tool a systematically cut all 33 first ...

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1 answers
0 votes
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Standalone Blast+; Automating searches, Blastn formatting, interpretation
2 votes

You just have to change the output format using the -outfmt parameter. To have an output in a tabular format just use -outfmt 6. The resulting table have 12 columns containing the following ...

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3 answers
9 votes
3k views
What is a quick way to find the reverse complement in bash
2 votes

You may either install the emboss package (http://emboss.sourceforge.net/download/) and use the revseq program. It contains many useful command-line programs such as the pairwise alignment tool needle....

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2 answers
3 votes
148 views
Merge / Reconciliate several de novo transcriptome assemblies with different kmers
1 votes

You may combine all your transcriptomes into a single file and then apply a clustering method to group very similar transcripts into a single one. For that purpose, you may try CD-HIT-EST or MMseqs2. ...

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1 answers
1 votes
131 views
Decontaminating RNA seqs for de novo transcriptome assembly and annotation of novel eukaryotes
1 votes

according to your Fastqc files, your reads have a moderate quality. But I am sure there is something to do to improve them. Try to run fastp with the following options: fastp -i _1.fq -I _2.fq --...

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1 answers
1 votes
74 views
How can I get unmatched reads for defective genomes analysis using bwa and samtools?
1 votes

If you want to keep track of the unmapped reads, I recommend you to use Bowtie2 instead of bwa. Start by building an index: bowtie2-build genome.fa genome.fa Then map your reads, using arguments to ...

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1 answers
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Finding out-group in unrooted tree
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1 votes

the fact is that the present upgma tree as a midpoint rooting here, corresponding to node 46. getRoot(upgma.a) so for this kind of tree, I recommend you to use the midpoint() rooting function. pars....

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2 answers
0 votes
85 views
merge rows (to columns) in R dataframe based on IDs
1 votes

For that purpose, you may also use the reshape2 R package which allows you to switch wide to long format for data.frames. However, for that, you need an additional column with sample identifiers, e.g.:...

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1 answers
1 votes
135 views
Adding external annotation to the phylogeny tree
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1 votes

there are nice features in R ggtree package. You may use the geom_cladelabel() function for your purposes. But I haven't find yet a way to automatize clade annotation. To do it, you have to be sure of ...

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2 answers
1 votes
35 views
Identify differentially covered genes only between two samples
1 votes

You may run edgeR for methylation analysis without replicates (https://f1000research.com/articles/6-2055). But I also recommend you to have a look at the R DSS package (http://bioconductor.org/...

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2 answers
0 votes
63 views
Tools for creating gene coexpression networks
1 votes

it depends on the size of your data. If you have enough RAM available, then you may directly compute a correlation-based distance matrix using the cor() function (with method="spearman" or method="...

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1 answers
1 votes
701 views
remove sequences from fasta file matching a string in the header
1 votes

you may use simple R commands, using the 'seqinr' package #load package library(seqinr) #load file containing sequences data<-read.fasta("filename.fa") #create a vector containing species names: ...

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2 answers
1 votes
168 views
How to transform and sort the matrix to make a heatmap showing signatures?
0 votes

You may also use the excellent pheatmap package. It is highly customizable, so do not hesitate to look at its help page and examples found therein. The code may look like this: library(pheatmap) data&...

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2 answers
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147 views
Difference between PPI networks and Gene Co-expression networks
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Co-expression networks are based on gene expression data. Genes are compared using their expression profiles over multiple samples. A common distance measurement is the Pearson Correlation Coefficient,...

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2 answers
1 votes
740 views
What is outliers and how to determine outliers in the following phylogenetic tree?
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you may use the OD-seq algorithm to filter outliers in a multiple alignment. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0702-1

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3 answers
1 votes
196 views
Filtering VEP annotation file
-1 votes

If you are working under a Linux environment, then you may easily use a piped grep search. For example: grep deleterious file.vcf |grep damaging >filtered_file.vcf

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