User: erwan.scaon

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erwan.scaon380
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Limoges - CBRS - France
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http://www.unilim.fr/r...
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1 day, 9 hours ago
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5 years, 9 months ago
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Posts by erwan.scaon

<prev • 35 results • page 1 of 4 • next >
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Answer: A: how to annotate RNA-seq
... To answer your first question : Create a TSV file with your input => list.tsv Remove ".13" etc from your ENSG (list.tsv) => list_ensembl_gid.tsv awk -F '\t' -v OFS='\t' '{sub(/\.[0-9]*/, "", $1)} 1' list.tsv > list_ensembl_gid.tsv; Then use R & Biomart to retrieve correspondi ...
written 2 days ago by erwan.scaon380
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Answer: A: How to convert gff file to a csv file
... You could try this : awk -F '\t' -v OFS=, '!/^#/ {$1=$1;print}' file.gff > file.csv; It will ignore lines starting with '#" in your GFF and convert tab to comma ...
written 8 days ago by erwan.scaon380
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Comment: C: biomaRt mmusculus_gene_ensembl dataset
... > I followed the advice and ran listDatasets(). Not surprisingly, > mmusculus_gene_ensembl is not there. It seems to be there currently : ensembl=useMart("ENSEMBL_MART_ENSEMBL") listDatasets(ensembl)[1] > dataset > 1 amelanoleuca_gene_ensembl > 2 dordii_gene_e ...
written 5 weeks ago by erwan.scaon380
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Answer: A: biomaRt mmusculus_gene_ensembl dataset
... > I'd assume that Mouse C57BL/6NJ is closest to the previous mmusculus Be cautious, if you need Ensembl gene / transcript identifiers (such as ENSG.., ENST...), the "Mouse C57BL/6NJ genes" dataset will not do the trick : library('biomaRt') mc57bl6nj = useMart("ENSEMBL_MART_MOUSE", ...
written 5 weeks ago by erwan.scaon380
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Comment: C: Balanced, nonredundant set of bacterial genomes
... Isn't [ncbi refseq][1] what you are looking for ? > a curated, non-redundant collection of reference sequences Or maybe you can look into previous consortium effort to get non-redundant DB, such as [HMP][2]. *Nb* : In case you want to download bacterial refseq, **here is the recipe** : ...
written 5 weeks ago by erwan.scaon380
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Trying to map informations between two Mus musculus strains with biomaRt external_gene_name field
... Dear all, I am trying to "map" *Mus musculus* infos between two strains (C57BL/6J & 129S1/SvImJ) based on biomaRt "external_gene_name" field. Using : Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28) biomaRt ‘2.34.0’ Commands : **Retrieve C57BL/6J infos :** b6 = useMart("E ...
ensembl biomart 129s1/svimj external_gene_name written 7 weeks ago by erwan.scaon380 • updated 7 weeks ago by Mike Smith440
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Read pair orientation : Illumina TruSeq Stranded mRNA library
... Given strand-specific 2x150 paired reads generated with Illumina Truseq Stranded mRNA, chose the right value for featureCounts "strandSpecific" option (1=stranded vs 2=reversely stranded). Below is a compilation of helpful posts on the subject. They made me pick strandSpecific = 2. I am under the ...
featurecounts truseq strandspecific written 8 weeks ago by erwan.scaon380 • updated 7 weeks ago by igor5.0k
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Comment: C: Looking for a thorough annotation for non-primary assembly units in GRCm38
... The first thing I see myself trying here is removing the 3 IgH alt scaffolds (GL456068, GL456078 & GL456017) from the reference genome. We suppose that the C57BL/6J primary assembly unit is close enough to the alt scaffolds, allowing reads originating from a 129S1/SvImJ IgH locus to map on the ...
written 8 weeks ago by erwan.scaon380
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Comment: C: Looking for a thorough annotation for non-primary assembly units in GRCm38
... To get a glimpse of what we are potentially losing atm with featureCounts given the lack of annotations for IgH alt scaffolds (GL456068, GL456078 & GL456017), I ran samtools (on 20 BAMs from 20 samples) on the GRCm38.p6 region (chr12:113067904-114458697) which have the 3 IgH alt scaffolds : ...
written 8 weeks ago by erwan.scaon380
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Comment: C: Looking for a thorough annotation for non-primary assembly units in GRCm38
... You mean creating our own annotation (GTF/GFF) for all the things contained inside the 1390793 nts of GL456017.2 ? I am not sure if this is doable or not yet. Edit : Yes, GL456017.2 is a separated entry (sequence). ...
written 8 weeks ago by erwan.scaon380

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Scholar 8 days ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
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Scholar 9 weeks ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
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