User: ignazio.fontana

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Posts by ignazio.fontana

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Comment: C: filter transcript isoforms with low support
... Thanks a lot. Can you indicate to me some software to do it? ...
written 8 weeks ago by ignazio.fontana0
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filter transcript isoforms with low support
... Hi, I need to filter transcript isoforms of my de novo assembled transcriptome with low support by removing isoforms minor of a percentual of the Trinity gene subcomponent read support. (in my case 0.01%) What is the correct strategy? I never made that. Thanks ...
filter rna-seq assembly written 11 weeks ago by ignazio.fontana0 • updated 11 weeks ago by kristoffer.vittingseerup2.3k
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(Closed) fasta header trimming in a multifasta
... Hi, I have a multifasta with the transcripts of an assembled rnaseq and the header of each fasta is like this: >TRINITY_DN5895_c0_g1_i1 len=288 path=[152:0-287] [-1, 152, -2] I want to trim each fasta header to: >TRINITY_DN5895_c0_g1_i1 Can you help me? Thanks ...
fasta header trim written 3 months ago by ignazio.fontana0 • updated 3 months ago by RamRS24k
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Number of genes in a kegg pathway
... Hi, how can I know for a kegg pathway how many genes are in? I need to know the percentage of genes that are covered in a pathway with the genes that i found in a transcriptome. Thanks ...
pathway genes kegg rna-seq written 3 months ago by ignazio.fontana0 • updated 3 months ago by predeus1.2k
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Novaseq 6000 paired end data Trimming and clipping
... Hi, I have 6 couples of paired end libraries (rnaseq) from Novaseq 6000. It is the first time I work with this kind of data; I read the header of my fastq and they have a double index. What software can I use to trimming adapters? Can I use trimmomatic and what adapters reference file I have to use? ...
novaseq adapters trimming rna-seq filtering written 6 months ago by ignazio.fontana0

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