User: YOUSEUFS

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YOUSEUFS10
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Posts by YOUSEUFS

<prev • 10 results • page 1 of 1 • next >
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Comment: C: GFF file multiple features for 1 gene region, how to collapse into 1?
... Thank you very much! ...
written 8 weeks ago by YOUSEUFS10
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GFF file multiple features for 1 gene region, how to collapse into 1?
... Hello, Noob here My GFF3 file (Converted into BED) contains multiple lines that describe the same gene region but with varying feature ID's (Below) NC_002978.6 3027 3115 gene2 . + RefSeq gene . ID=gene2;Dbxref=GeneID:29555340;Name=WD_RS00025;gbkey=Gene;gene_bi ...
bedtools gff rna-seq written 8 weeks ago by YOUSEUFS10 • updated 8 weeks ago by Carambakaracho660
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Comment: C: Aligning Draft to Reference genomes, rearranging contigs?
... I don't know to be honest, I'm just checking from more experienced people than myself to see if it would =) ...
written 13 months ago by YOUSEUFS10
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Aligning Draft to Reference genomes, rearranging contigs?
... Hello Bioinformagicians! My end goal is to map some RNA-seq data to a genome iv'e been given but I do not know if this genome is assembled in the right order. In order to analyse this, I'm attempting to align a draft genome sequence (containing contigs and scaffolds) to a closely related reference ...
assembly mummer alignment written 13 months ago by YOUSEUFS10
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Mapping contigs & scaffolds to ref genome?
... Noob here, I'm trying to map a file of contigs and scaffolds onto a reference genome but bowtie keeps outputting the same error: bowtie2 -f -x wmel_genome -U ~/Aa23/ref/assemblies/wMelPopPGYP.finalassembly-alt.fasta > terminate called after throwing an instance of 'std::bad_alloc' > ...
assembly mapping bowtie2 written 14 months ago by YOUSEUFS10 • updated 4 months ago by h.mon22k
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Comment: A: .nt assemblage file, can I convert to FASTA?
... The first few lines look like this (it might not show correctly here) ....|....| ....|....| ....|....| ....|....| ....|....| ....|....| 5 15 25 35 45 55 scaffold00 ttggttaggt aaggaagtag tattgctact actccctccc ttagaaacgc agcatgcagg ...
written 14 months ago by YOUSEUFS10 • updated 14 months ago by Pierre Lindenbaum115k
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.nt assemblage file, can I convert to FASTA?
... Hi all I've been given a .nt (never come across these before) file of a bacterial genome which I want to index to use with bowtie but bowtie accepts .fasta and not .nt. Could you guys explain what the hell a .nt file is and can I convert it to .fasta? Huge thanks in advance! ...
fasta file usage bowtie mapping written 14 months ago by YOUSEUFS10
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htseq-count results in missing genes
... Hello Bioinformatics wizards! I've recently counted my aligned reads w/ htseq-count and I am now placing them in excel next to their PROKKA gene ID's to see what genes these reads are actually aligning to. I'm noticing that out of the 1080 genes 37 of them are missing in my htseq-counts. Genes wit ...
htseq-count rna-seq written 16 months ago by YOUSEUFS10
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Comment: C: Visualising indexed and sorted bam files
... Thank you very much! ...
written 16 months ago by YOUSEUFS10
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Visualising indexed and sorted bam files
... I'm a new PhD student and bioinformatics is all very new to me so apologies if this seems trivial. I have some paired-end RNA-seq data which I've managed to convert to sorted and indexed bam files however I'm confused to where I go from here, am I right in thinking I can now visualise this data and ...
rna-seq written 16 months ago by YOUSEUFS10 • updated 16 months ago by Charles Plessy2.6k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Mapping contigs & scaffolds to ref genome?

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