User: Buffo

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Buffo590
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590
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1 year, 8 months ago
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Posts by Buffo

<prev • 166 results • page 1 of 17 • next >
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Comment: C: How to predict a structure if it is less than 30 aminoacids long?
... That is not a mutation, is a deletion, furthermore "protein" of 25 aminoacids is a functional protein? I think you can't predict 3D structure because it doesn't exist, it is more a polypeptide than a protein. ...
written 16 days ago by Buffo590
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Comment: C: Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
... I had the same problem, however it is solved for version 1.3.3, merge is not necessary anymore. ...
written 17 days ago by Buffo590
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Comment: C: how to cluster genes in heatmap
... a very good example of a clustered [heatmap][1] [1]: https://www.biostars.org/p/238128/ ...
written 20 days ago by Buffo590
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HISAT2 indexes, GRCm38 or mm10?
... Hi everybody, Somebody knows which is the difference between GRCM38 and mm10 genomes? There are both [HISAT2][1] indexes. Which is the difference? Thanks [1]: https://ccb.jhu.edu/software/hisat2/manual.shtml ...
hisat2 rna-seq index written 20 days ago by Buffo590 • updated 20 days ago by Sej Modha2.3k
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Comment: C: Multiple fastq alignment with bowtie2
... ......... -q $i -S $i.sam instead of: path_to_my_fastq_file/*.fastq ${i}.fastq ...
written 20 days ago by Buffo590
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Answer: C: miRDeep2 out put
... is normalized read count, TPM is dependent to transcript lenght and from miRNA-seq you don´t have it, you cannt use it. At least you are looking for precursos more than mature mirnas and perform the assembly. ...
written 23 days ago by Buffo590
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Comment: C: Is there any plant-specific genome assembler?
... You will need a powerful machine (specially RAM memory) more than special assembler, at least pine genome are expected to be in the order of 20 Gb :). ...
written 24 days ago by Buffo590
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Comment: C: Tools for visualizing genome
... IGV and find motif function would be a fast insight. ...
written 24 days ago by Buffo590
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Comment: C: Sequence retrieval from miRBase using miRBase sequence ids
... download the data from mirbase [ftp][1] and then write a fast python script such as: my_list = [miR1171, miR1436, miR1439, miR1446, miR1446a...] seq = '' with open(sys.argv[1], 'r') as fasta: for line in fasta: line = line.rstrip('\n') if line.start ...
written 25 days ago by Buffo590
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... It is able to assemble long sequences from PacBio or miION, I don't think that you can find a specific software for doing exactly what you are looking for. Longer scaffolds from scaffolds? or even if you find a software to do that I think you will need lots of further karyotype validations to use yo ...
written 26 days ago by Buffo590

Latest awards to Buffo

Supporter 4 months ago, voted at least 25 times.
Scholar 7 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Centurion 7 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: How can I get FASTA if i have Names of proteins ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How can I get FASTA if i have Names of proteins ?

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