User: edoardo.piombo

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Posts by edoardo.piombo

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Comment: C: Tool for transcription factor driven prediction of binding sites
... Thank you! I will check them out! ...
written 12 months ago by edoardo.piombo20
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Comment: C: Tool for transcription factor driven prediction of binding sites
... Ok, so maybe I did not express myself well: I have no idea about which are the binding sites of my transcription factor. I know it is a putative transcription factor by blast alignments and interproscan analysis, and I suspect it is involved in the regulation of a specific set of genes due to its po ...
written 12 months ago by edoardo.piombo20
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Comment: C: Tool for transcription factor driven prediction of binding sites
... Hi! First of all thank you for the suggestions, I'm doing all of that, but I have a question: how do I determine which is my motif of interest, starting from the sequence of my transcription factor? Sure, I can use MEME on the promoter sequences and then use TOMTOM to compare my motives with various ...
written 12 months ago by edoardo.piombo20
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Tool for transcription factor driven prediction of binding sites
... Hi everybody! I have a fungal transcription factor, and I suspect it is a negative regulator of a certain set of genes: do you know any tool that might help me look for binding sites in a transcription factor driven way? All the tools I am finding work on the promoter sequence of the target genes ...
transcription factor promoter binding sites written 12 months ago by edoardo.piombo20 • updated 12 months ago by Alex Reynolds29k
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Can anyone suggest me a good pipeline to perform SNP calling on haployd organisms?
... Hi, I was wandering if anyone might suggest me a good pipeline to perform SNP calling on haployd organisms. I am currently using this one: samtools mpileup -guf reference_genome.fa target_organism.sort.bam | bcftools view -cg - | vcfutils.pl varFilter –Q 20 - > result_vcf ...
snp calling comparative genomics snp mining written 2.6 years ago by edoardo.piombo20 • updated 2.6 years ago by WouterDeCoster42k
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Comment: C: Problem using SnpEff after Transdecoder: large number of warnings
... Understood. I apologize again for the cross posting. I tried to remove the thread from Seq Answers but it seems that I am unable to do so. Thanks for your advice on the question, I tried to remove the transcript whose CDS didn't start with a start codon and the warnings disappeared, but to do so I h ...
written 3.0 years ago by edoardo.piombo20
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Comment: C: Problem using SnpEff after Transdecoder: large number of warnings
... I'm very sorry, I didn't know it would be annoying. Which site do you think is the best to contain the question? I will promptly remove it from the other one. ...
written 3.0 years ago by edoardo.piombo20
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Problem using SnpEff after Transdecoder: large number of warnings
... Hi, I am a PhD student with very little experience in bioinformatics (or very little experience at all, I started two months ago). I’m having some problems getting Snpeff to work with gff coordinates obtained by Transdecoder. I was given by a group with which I am collaborating the assembly of a ge ...
R rna-seq snp cds finding written 3.0 years ago by edoardo.piombo20 • updated 3.0 years ago by genomax74k

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