Moderator: h.mon

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h.mon9.7k
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Posts by h.mon

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Comment: C: Counting nucleotide frequency using perl script
... First, `use strict;`, it will save you a lot of headache. Second, I guess this script was created for fastq files ( `if($count eq 4){` ), but you are using it for fasta files. Finally, a more readable (for me, at least) way of counting characters is: my $seq = "aaATATGAAGCTc"; my $Acount ...
written 43 minutes ago by h.mon9.7k
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Answer: A: How to simulate RNA-seq raw read counts matrix
... I found a couple of alternatives, maybe one of them will fit your needs: [SimSeq][1], or maybe you could modify [DESeq::makeExampleCountDataSet][2] to suit your needs. P.S.: also [compcodeR::generateSyntheticData][3] [1]: https://cran.r-project.org/web/packages/SimSeq/SimSeq.pdf [2]: https:// ...
written 2 hours ago by h.mon9.7k
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Comment: C: blast and update_blast.pl (nr files): No alias or index file found for protein d
... Could you copy / paste the exact update_blastdb and blast commands, and the error message? Did you uncompressed the database after downloading? ...
written 2 hours ago by h.mon9.7k
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Answer: A: Detect LINE1 element in NGS data
... Have a look at [TEToolkik][1] or [SalmonTE][2]. I am sure the [gtf][3] annotation provided by the TEToolkit team includes LINEs, I believe - but don't know for sure - SalmonTE should also include them. [1]: http://hammelllab.labsites.cshl.edu/software/#TEToolkit [2]: https://github.com/hyunhwa ...
written 7 hours ago by h.mon9.7k
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Comment: C: stranded vs not stranded Htseq-output differences
... "Directional RNAseq" is not the name of a library prep kit. But taking into account "Directional RNAseq" and your counts, you have to use `stranded=reverse`. If you are so overwhelmed at this step, I strongly suggest you should contact a local bioinformatician for help / teaching / collaboration. ...
written 7 hours ago by h.mon9.7k
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Comment: C: stranded vs not stranded Htseq-output differences
... You are welcome. > I am so confused with these results. Did you try it? I am sure it would help clarify your confusion. Besides, something I should have asked from the beginning: what kit did you (or your sequencing provider) used to prepare the sequencing library? ...
written 8 hours ago by h.mon9.7k
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Answer: A: How Hisat Works
... Do you already understand the Burrows-Wheeler Transform? Not at child level, but two very good explanations: http://spencer-carroll.com/an-easy-to-understand-explanation-of-the-burrows-wheeler-transform/ http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods http://b ...
written 9 hours ago by h.mon9.7k
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Comment: C: koeken intall problem
... > If you have MacQIIME installed, you must first initialize it before installing Koeken. If you do not have macqiime installed, you can still run koeken as long as you have the scripts available in your path. Did you follow these instructions? ...
written 11 hours ago by h.mon9.7k
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Comment: C: How RSEM define gene
... Could you show the command-lines of your complete pipeline? ...
written 22 hours ago by h.mon9.7k
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Comment: C: samtools vs bedtools
... Your question is not silly, but is poorly formulated, and suggests you made little effort to find the answers. For example, `samtools depth` vs `bedtools genomecov` has been discussed many times (e.g. [avrilomics][1] blog, on [biostars][2] or bioinformatics [stackexchange][3]). Please read [Tutorial ...
written 22 hours ago by h.mon9.7k

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Scholar 9 hours ago, created an answer that has been accepted. For A: gage and pathview : genes are not mapped
Scholar 1 day ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Appreciated 1 day ago, created a post with more than 5 votes. For A: Converting TCGA expression data from FPKM to TPM
Popular Question 3 days ago, created a question with more than 1,000 views. For gff format to genome annotation
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Popular Question 5 days ago, created a question with more than 1,000 views. For gff format to genome annotation
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: Converting TCGA expression data from FPKM to TPM
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Scholar 8 days ago, created an answer that has been accepted. For A: gage and pathview : genes are not mapped
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
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Scholar 10 days ago, created an answer that has been accepted. For A: gage and pathview : genes are not mapped
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Scholar 15 days ago, created an answer that has been accepted. For A: gage and pathview : genes are not mapped
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Popular Question 26 days ago, created a question with more than 1,000 views. For gff format to genome annotation
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
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Scholar 8 weeks ago, created an answer that has been accepted. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Scholar 9 weeks ago, created an answer that has been accepted. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem

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