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Recent Replies
Comment: Slot to pull data from for DoHeatmap
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use the data slot, and as shown in the code, you then scale it by yourself.
Answer: Example human WGS fastq data
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Take a look at Genome in a Bottle https://www.nist.gov/programs-projects/genome-bottle
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I would suggest you to use fastq-dl https://github.com/rpetit3/fastq-dl to download at project level
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use bowtie1 for short reads
https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1/
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I understand you have a steep learning curve...you should learn how to use blast from a command line.
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Hi Michael, I still cannot download.
Actually I want to download E-MTAB-6798 from ENA.
https://www.ebi.ac.uk/biostudies/arrayexpress/…
Comment: Alignment tool for very short reads (25bp)
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Thank you very much for your reply.
Comment: Alignment tool for very short reads (25bp)
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arriyaz.nstu
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Thank you too for a very nice and clear suggestion. Sure, I will check the `bowtie2` options.
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Thanks! I think you might be misinterpreting your coverage output. I believe that just indicates the chromosome and how many reads map to i…
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Not sure. May be some files are corrupted.
How about try
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There are two sequences per entry, and the provided awk script has merged the two sequences into a single linear sequence. But the objectiv…
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Using @yokofakun 's [**linearize fasta code**][1]
awk '/^Lm/ {printf("%s%s\t",(N>0?"\n\n":""),$0);N++;next;} {printf("%s",$0);} END …
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That is very few reads. Are you sure your run was successful?
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bowtie aka bowtie1 was developed when these very short reads were state of the art. Id give that a try and see what comes out. Multithreade…
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> What are other reliable tools for the alignment of DNA reads with very short lengths (25-50bp)?
[vmatch][1]
[1]: http://www.vma…
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