User: Chvatil

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Chvatil50
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2 years, 6 months ago
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b****************@gmail.com

Posts by Chvatil

<prev • 144 results • page 2 of 15 • next >
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Comment: C: Size of the nr database fasta file?
... Thank you very much for the answer ...
written 3 months ago by Chvatil50
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Size of the nr database fasta file?
... Hello everyone, I'm trying to download the database nr and it is still downloading in fact and its size is actually `100Gb` So I think this is a good question for those who want to know how to estimate the disk space needed to download all the `fasta file`? So if anyone knows where I can find th ...
ncbi database nr written 3 months ago by Chvatil50 • updated 3 months ago by brian.fristensky130
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Eucaryotic gene predictor within eucaryote genome
... Hello everyone, I created this post to ask you some advice to find a suitable tool. Indeed, I am looking for a program that can predict *eukaryotic genes* in an **assembled genome.** I know **Augustus3.3** for example but I can't find a statistical confidence metric related to the predicted genes. ...
gene written 3 months ago by Chvatil50 • updated 3 months ago by Juke344.8k
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disable the SRA cache in HISAT2
... Hello, I found many posts talking about this subject but none of them explain how to do that. In fact I ran a **HISAT2** analysis on my data, for that I use the `--sra-acc` option with the sra IDS. Then I map these read against a fasta genome assembly. But during the process I get this error mes ...
rnaseq hisat mapping written 3 months ago by Chvatil50
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Comment: C: Test if a list of genes with coordinates are expressed (hisat2 data)
... Thanks but I have around thousand of candidate gene and I need to get a more general method .. ...
written 3 months ago by Chvatil50
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Test if a list of genes with coordinates are expressed (hisat2 data)
... Hello everyone, I need some help in order to know wether candidates genes are expressed or not. In order to do that I have already done the following steps : **3 Built hisat indexes** $HISAT2/hisat2-build Assembly.fa mapping_index **2 Mapper the RNA reads to the assembly** $HISAT2 ...
rna-seq transcription written 3 months ago by Chvatil50 • updated 3 months ago by khorms130
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Comment: C: Using Bowtie and SRA mode
... It is the same, this is the option that is not recognized ...
written 4 months ago by Chvatil50
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Comment: C: Using Bowtie and SRA mode
... I tried to dowload `wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/bowtie2-2.4.1-linux-x86_64.zip` but I still get the same issue it does not recognise the '--sra-acc' option... ...
written 4 months ago by Chvatil50
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Comment: C: Using Bowtie and SRA mode
... I built my db with : /beegfs/data/my_conda/bin/bowtie2-build -f /beegfs/data/Genomes/Vcanescens/Vcanescens.fa Bowtie_db_Vcanescens then I ran : /beegfs/data/my_conda/bin/bowtie2 -x /beegfs/data/Genomes/Vcanescens/Bowtie_db_Vcanescens -S /beegfs/data/Genomes/Vcanescens/Mapping/Bowtie_ ...
written 4 months ago by Chvatil50
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Using Bowtie and SRA mode
... Hello I need to map reads on a genome in fasta file format. For that I installed `Bowtie2 v2.4.1`(last version) with biodonda by doing : conda install bowtie2 Everything went right and I can run bowtie2 properly. But I need to use the `--sra-acc` option and in the documentation they say : ...
mapping bowtie written 4 months ago by Chvatil50

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Get summary of augustus ouput (gff)
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Popular Question 4 months ago, created a question with more than 1,000 views. For Issue using MaSuRCA-3.2.6
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