User: Federico Giorgi

gravatar for Federico Giorgi
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Columbia University
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8 years, 9 months ago
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Posts by Federico Giorgi

<prev • 40 results • page 1 of 4 • next >
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News: Call for Bioinformatics Papers - Genes Special Issue
... Hi all! My name is Federico Giorgi, I'm a newly appointed Professor of Bioinformatics at the University of Bologna (Italy) and I'm trying to give my little contribution push Bioinformatics upwards and beyond! The editor MDPI gave us the responsibility to edit the next special Issue of Genes (IF 3. ...
gene news written 6 months ago by Federico Giorgi590
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Consensus sequence from multiple BAM files on a single position
... Hi all, I have several thousands sorted BAM files and I would like to quickly extract the consensus sequence from all the reads on a specific position. Simply using samtools view provides all the reads (including those jumpoing the position due to splicing). I could not make it work via mpileup. He ...
bam samtools mpileup written 9 months ago by Federico Giorgi590 • updated 9 months ago by jkbonfield380
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Comment: C: Show RNASeq coverage distribution over transcript length
... Nice but what's on the y-axis? Is it relative per-transcript read coverage? Why is it negative? It is a nice tool, but what I'm really looking for is a transcriptome-wide assessment of uneven transcript coverage, as a quality assessment of 5' degradation. I guess I will just leave this question open ...
written 2.0 years ago by Federico Giorgi590
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Show RNASeq coverage distribution over transcript length
... Hi all! I have RNASeq data aligned over a transcriptome in BAM format. Provided the gene annotation (GTF, GFF3), do you know of any tool that can show global transcript coverage with respect to the transcript length? I would like to quantify any uneven transcriptome-wide transcript coverage, speci ...
bam rna-seq transcriptomics sequencing written 2.0 years ago by Federico Giorgi590 • updated 2.0 years ago by Carlo Yague5.0k
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Answer: A: question about DiffBind
... Hi there, I believe you are using a not up-to-date example. In DiffBind 2.4.0+ you achieve what you want to do (i.e. loading the example sample sheet) like this: library(DiffBind) setwd(system.file("extra", package="DiffBind")) tamoxifen <- dba(sampleSheet="tamoxifen.csv") Check *? ...
written 2.1 years ago by Federico Giorgi590
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Answer: A: How To Download All Sra Samples At Once ?
... A non-R solution is to use the **[SRA toolkit][1]** *prefetch* command on a list of SRA identifiers. First you need the file list. You can batch download it. In your case, go to https://www.ncbi.nlm.nih.gov/sra?term=SRP026197 Top-right, click to "Send To", "File", "Accession List". Once you have i ...
written 2.1 years ago by Federico Giorgi590
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Answer: A: how to find new transcript from bam file?
... Cufflinks used to be the most popular, but I would suggest StringTie (also from Johns Hopkins University), because it is more accurate for intronic and intron-retaining transcripts. They both require a BAM file as input and an optional transcript track annotation file (GFF3 or GTF) [Cufflinks][1] ...
written 2.1 years ago by Federico Giorgi590
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Answer: A: download from SRA
... You can use xargs and the sra-toolkit prefetch to download every SRR id contained in a txt file list, like: xargs -n1 prefetch < SRR_Acc_List.txt ...
written 2.2 years ago by Federico Giorgi590
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SNP/indel annotation in Arabidopsis
... Hi all, I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. knowing which ones can cause an aminoacid change or an early stop, using the default Arabid ...
indel varscan arabidopsis snp written 2.2 years ago by Federico Giorgi590 • updated 2.2 years ago by finswimmer13k
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Answer: A: Vertebrate Subset Nr Database? Build My Own?
... A blast+ solution to this problem is the following 1. download your database from the NCBI ftp website (e.g. nt) 2. download a list of GI identifiers from entrez 3. extract the fasta sequences using blastdbcmd ``` blastdbcmd -db nt -dbtype 'nucl' -entry_batch $gilist -out vertebrates.fa ``` 4. ...
written 6.4 years ago by Federico Giorgi590 • updated 10 months ago by RamRS27k

Latest awards to Federico Giorgi

Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How To Download All Sra Samples At Once ?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Appreciated 19 months ago, created a post with more than 5 votes. For A: How To Download All Sra Samples At Once ?
Prophet 19 months ago, created a post with more than 20 followers. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Blast Output With Species Name
Great Question 24 months ago, created a question with more than 5,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Differential Expression Analysis On Rpkms - Contrasts And Contrasts Of Contrasts
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Blast Output With Species Name
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Vertebrate Subset Nr Database? Build My Own?
Good Question 4.6 years ago, asked a question that was upvoted at least 5 times. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Appreciated 4.9 years ago, created a post with more than 5 votes. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Epic Question 4.9 years ago, created a question with more than 10,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Great Question 6.1 years ago, created a question with more than 5,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Differential Expression Analysis On Rpkms - Contrasts And Contrasts Of Contrasts
Student 6.1 years ago, asked a question with at least 3 up-votes. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 6.4 years ago, voted at least 25 times.
Commentator 6.4 years ago, created a comment with at least 3 up-votes. For C: How Are Transposable Elements Marked In A Genome?
Teacher 6.4 years ago, created an answer with at least 3 up-votes. For A: Blast Output With Species Name
Student 6.4 years ago, asked a question with at least 3 up-votes. For Differential Expression Analysis On Rpkms - Contrasts And Contrasts Of Contrasts

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