User: joangibert14

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Posts by joangibert14

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Comment: C: Get 3'UTR sequence using RNAseq read coverage
... Uhm, the feature column in the output should. At least is what it claims in the documentation, right? Anyway, I am not sure what you are referring to. Is something like comparing the two gtf files (the mouse reference and the stringtie output) and get the lines from the second that are not in the f ...
written 5 months ago by joangibert140
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Comment: C: Get 3'UTR sequence using RNAseq read coverage
... I tried `stringtie` with gencode gtf for mouse. The file I got does not have any line with UTR feature. The gtf contains this information and also when I check the bam files in IGV I see reads in the UTRs. Any idea what is going on? ...
written 5 months ago by joangibert140
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Get 3'UTR sequence using RNAseq read coverage
... Hi! I have some bam files aligned to mouse reference genome. I want to analyze some motif enrichment in the 3'UTR of this samples but I realize that some mRNA have longer 3'UTR than the reference genome. I double checked this an is something reported in platelets that is what I'm working. Is there ...
rna-seq written 5 months ago by joangibert140 • updated 5 months ago by kristoffer.vittingseerup2.2k
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Answer: A: Modify IOT formated VCF by the most frequent variant
... I kind of solve it using vcfR package. If anyone would need to do this in the future, here is the issue: https://github.com/knausb/vcfR/issues/112 ...
written 12 months ago by joangibert140
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Thanks for your help! As you may suppose, managing vcf files is quite new to me... Here's an input example: https://gist.github.com/Tato14/ce1f2ab9c38c63a201ba1756a5e20dd8 ...
written 13 months ago by joangibert140
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Hi Pierre! Thanks for the formatting. > I would like to get rid of the rest of the variants. Means that I only want to keep only one COSMIC ALT allele (the one with bigger AF). I wasn't aware of the `Number=A`. Here's an output example: CHROM POS ID REF ALT QUAL FILTER INFO FO ...
written 13 months ago by joangibert140
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Modify IOT formated VCF by the most frequent variant
... I have a VCF from the IOT server analyzer which look like (I paste just one entry for a call of a variant in KRAS gene): CHROM POS ID REF ALT QUAL FILTER INFO FORMAT chr12 25398280 COSM536;COSM535;COSM12655;COSM537;COSM12721;COSM531;COSM87280;COSM532;COSM528;COSM523;COSM521;COSM25081;COS ...
vcf R snp bash written 13 months ago by joangibert140
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Comment: C: Remove entries in a IRangesList
... Hi! Thanks! It worked for me without the `unlist` function. And yes, `` gives the chromosome information :). ...
written 13 months ago by joangibert140
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Remove entries in a IRangesList
... Hi! I have an IRangesList with several entries like: [[1]] IRanges object with 1 range and 8 metadata columns: start end width | tx_id cds_ok exon_id exon_rank seq_start seq_end | -1 -1 1 | ENST ...
R written 13 months ago by joangibert140 • updated 13 months ago by ATpoint21k
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Comment: C: Get aminoacid sequence and position from genomic coordinates
... Hello Fin, I have the reference fasta (GRCh37) and the annotation file (in this case refGene). Also, I know which gene corresponds the region but this could change between samples so I don't know if this should be strictly necessary. Thanks for your help :) J ...
written 13 months ago by joangibert140

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Scholar 12 months ago, created an answer that has been accepted. For A: Modify IOT formated VCF by the most frequent variant

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