Moderator: genomax

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genomax28k
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Posts by genomax

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Comment: C: how install tools of galaxy shed to galaxy
... You should post this over at [Galaxy Biostars][1]. [1]: https://biostar.usegalaxy.org/ ...
written 10 hours ago by genomax28k
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Comment: C: Which files in the NCBI Genomes ftp site are the most reliable
... Since you need a fasta formatted sequence file for creating blast indexes I selected `.fna` file. `gbff` is genbank formatted version of the same genome. Read about what the different files are, [here][1]. [1]: ftp://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_other/Anolis_carolinensis/latest_ass ...
written 16 hours ago by genomax28k
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Comment: C: pacbio db and las files
... `DAMAPPER` is the program that is producing those files (https://dazzlerblog.wordpress.com/command-guides/damapper-commands/ ). ...
written 19 hours ago by genomax28k
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Comment: C: Problem running Fastortho Debian 8.7
... Please use `ADD REPLY/ADD COMMENT` when responding to existing posts to keep threads logically organized. Testing ORTHO install would not solve a problem (if one exists) but it will tell you if the install is otherwise correct and working as expected. ...
written 20 hours ago by genomax28k
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Comment: C: Differences between ensembl gtf files and gff3 file
... [GTF Format reference][1] from Ensembl. [GFF3 format reference][2] from GMOD. [1]: http://www.ensembl.org/info/website/upload/gff.html [2]: http://gmod.org/wiki/GFF3#GFF3_Format ...
written 2 days ago by genomax28k
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Comment: C: When I install samtools, the linux cannot find -lcurses and cannot find -lz. How
... As long as one accepts that there is a chance of not getting the latest version of a program, this is the least painful way. ...
written 2 days ago by genomax28k
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Answer: A: Asking for books for bioinformatics book for beginner
... For a "How to do X analysis" questions, there is [Biostars Handbook][1]. It is not free, but provides a practical introduction to bioinformatics analyses with a focus on high-throughput sequencing data. For other basic biology concepts/questions you can search the [Molecular Biology of the Cell boo ...
written 2 days ago by genomax28k
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Comment: C: QIIME - Illumina MiSeq, Paired-end Data - Mapping file and Data Preprocessing Qu
... Please use `ADD REPLY/ADD COMMENT` when responding to existing threads to keep them logically organized. Take at look at this link to see how to setup mapping file: http://qiime.org/documentation/file_formats.html ...
written 3 days ago by genomax28k
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Comment: C: To find Single Nucleotide polymorphism
... You want to use the BAM file which contains the alignment information. You don't want to extract the reads that mapped (which is what I assume you are alluding to?) See the section on `variant calling` on this page that shows how to use Samtools (http://www.htslib.org/workflow/ ). ...
written 3 days ago by genomax28k
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Comment: C: To find Single Nucleotide polymorphism
... > One important thing is in SAMtools they use bam files and I am looking > to use fastq files You can't wish for something and expect it to work. Since you realize that you must get the bam files from your fastq files, that is step 1 (hint: align your fastq files to a reference). ...
written 3 days ago by genomax28k

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Scholar 2 days ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
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Scholar 3 days ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
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Scholar 28 days ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
Scholar 4 weeks ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Better for my career: Degree in computer science or Phd in bioinformatics?
Scholar 5 weeks ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?

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