User: Neuls

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Neuls0
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Posts by Neuls

<prev • 16 results • page 1 of 2 • next >
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RNAseq consensus transcript sequence
... Dear all, I have a RNA seq pair-end data from a bacteria. I mapped the data against a well-known reference genome using bowtie2. Then, I converted and sorted the resulting .sam file to .bam using samtools and I assembled the transcripts using StringTie: samtools view -u bowtie2.sam | samtools ...
assembly alignment rna-seq written 6 months ago by Neuls0
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Comment: C: Hisat2 overall alignment rate below 50%
... I carried on the analysis as similar as I could according to the paper info, which was very limited. The information regarding to the preproceesing and mapping is what you can read in the post 1, 2) they do not mention the reference genome as well as the mapping results of tophat. I blasted like 10 ...
written 6 months ago by Neuls0
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Hisat2 overall alignment rate below 50%
... Dear colleagues, I am working on transcriptome reassembly of four bacterial strains from a study which has been published recently. I have downloaded the .sra files and converted them to .fq using `fastq-dump --split-files`, since they are pair-end reads 75pb each. In the paper the authors mention: ...
assembly rna-seq sequencing written 6 months ago by Neuls0 • updated 6 months ago by h.mon26k
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Comment: C: Xscore Installation Issue using Bash
... It is not working, same error as before ...
written 9 months ago by Neuls0
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Comment: C: Xscore Installation Issue using Bash
... They are : -rw-r--r-- 1 marta marta 38801 mag 25 2016 RESIDUE_DEF_XTOOL. Is it a permission problem? ...
written 9 months ago by Neuls0
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Xscore Installation Issue using Bash
... Dear all, I am trying to install xscore v1.3 ([Xscore Manual][1]). They provide instructions to set up some environmental variables in the .cshrc file under C-shell. setenv XTOOL_HOME the_installation_directory_of_X-Score setenv XTOOL_PARAMETER $XTOOL_HOME/parameter setenv XTOOL_BI ...
installation csh c shell xscore bash written 9 months ago by Neuls0 • updated 8 months ago by John Marshall1.6k
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Protein flexibility B factor
... I was asked to search for epitopes in a protein and assess if they were flexible. To my knowledge i have mainly one possibility which would be doing MD and calculate the rmsf and rmsd for the region of insterest (I have no clue about time scale.. im short on computational power) However, i wonder i ...
protein flexibility b-factor written 14 months ago by Neuls0
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jModelTest - Interpreting its outputs
... Hi, I ran jModeltest program in order to choose the model that best fits my data using different selection criteria (AIC, BIC..). I'm having trouble to interpret one of the outputs given by this program: ![jModeltest Output][1] For one model of substitution the program takes a summary comparing wh ...
jmodeltest substitution model phylogenetics written 2.0 years ago by Neuls0
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How can I download all NR fasta sequences corresponting to the same specie from NCBI?
... Hi, I'm interested on comparing 16S rna among some species so I'd like to download all NR_ fasta sequences from NCBI 16Sdatabase corresponding to a specie of interest. I have been reading about Enterz but I wonder if it can be done easly from a webrowser. So far I got sequences from Silva database ...
ncbi 16s nr entrez written 2.2 years ago by Neuls0
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cd-hit redundancy removal
... I'm planing to use cd-hit to remove redundancy from a 16S mRNA dataset I have got in order to build a philogenetic tree using Phylip later on. Maybe it is a newbiew question but I wonder if i have to remove redundacy before or after doing MSA using MAFFT. Also I wonder if the output from cd-hit ca ...
cd-hit redundancy written 2.4 years ago by Neuls0 • updated 2.4 years ago by Biostar ♦♦ 20

Latest awards to Neuls

Popular Question 5 months ago, created a question with more than 1,000 views. For cd-hit redundancy removal
Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogenetic Tree to compare my sequences to a database
Popular Question 6 months ago, created a question with more than 1,000 views. For Phylogenetic Tree to compare my sequences to a database
Popular Question 15 months ago, created a question with more than 1,000 views. For R for loop trouble with paste0 an variable assignment

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