User: Federico Giorgi

gravatar for Federico Giorgi
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Columbia University
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8 months, 2 weeks ago
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7 years, 10 months ago
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Posts by Federico Giorgi

<prev • 38 results • page 1 of 4 • next >
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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 13 months ago by Federico Giorgi500
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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 13 months ago by Federico Giorgi500 • updated 13 months ago by Carlo Yague4.6k
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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 14 months ago by Federico Giorgi500
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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 14 months ago by Federico Giorgi500
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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 15 months ago by Federico Giorgi500
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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 15 months ago by Federico Giorgi500
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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 16 months ago by Federico Giorgi500 • updated 16 months ago by finswimmer12k
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Answer: A: Vertebrate Subset Nr Database? Build My Own?
... A blast+ solution to this problem is the following download your database from the NCBI ftp website (e.g. nt) download a list of GI identifiers from entrez extract the fasta sequences using blastdbcmd blastdbcmd -db nt -dbtype 'nucl' -entry_batch $gilist -out vertebrates.fa create a new reduced b ...
written 5.5 years ago by Federico Giorgi500
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Answer: A: Co-Expression Networks Of Rna-Seq
... For simple correlation based networks you need at least 8-10 samples to be able to build some sort of network. So far the smallest networks accepted in literature using RNASeq data are those from Iancu (Mouse, 21 samples) and Giorgi (Arabidopsis, 65 samples) ...
written 5.7 years ago by Federico Giorgi500
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Answer: A: Blast Output With Species Name
... You may want to use the latest NCBI BLAST 2.2.28, which addresses specifically this issue! So in order to get species id you can change your outfmt format into: -outfmt '6 qseqid sseqid pident evalue staxids sscinames scomnames sskingdoms stitle' ...
written 5.8 years ago by Federico Giorgi500

Latest awards to Federico Giorgi

Great Question 13 months ago, created a question with more than 5,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Differential Expression Analysis On Rpkms - Contrasts And Contrasts Of Contrasts
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Blast Output With Species Name
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Vertebrate Subset Nr Database? Build My Own?
Good Question 3.8 years ago, asked a question that was upvoted at least 5 times. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Appreciated 4.0 years ago, created a post with more than 5 votes. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Epic Question 4.0 years ago, created a question with more than 10,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Great Question 5.2 years ago, created a question with more than 5,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Differential Expression Analysis On Rpkms - Contrasts And Contrasts Of Contrasts
Student 5.2 years ago, asked a question with at least 3 up-votes. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Extract Cds Fastas From A Gff Annotation + Reference Sequence
Supporter 5.5 years ago, voted at least 25 times.
Commentator 5.5 years ago, created a comment with at least 3 up-votes. For C: How Are Transposable Elements Marked In A Genome?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Blast Output With Species Name
Student 5.5 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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