Moderator: h.mon

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h.mon22k
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Posts by h.mon

<prev • 3,359 results • page 1 of 336 • next >
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Answer: A: Is there any open-source Illumina bacterial genome mapping and annotation websit
... The page http://www.theseed.org/servers/ mentions there is a package called "RASTserver.pm", you can search for this package and find more information. Also, the RAST blog has a post about the [The RAST batch interface][1]. [1]: http://blog.theseed.org/servers/usage/the-rast-batch-interface.html ...
written 46 minutes ago by h.mon22k
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Comment: C: Using VelvetOptimiser.pl within a forloop
... How come the output of for i in *_1_*.fastq; do echo '-fastq -shortPaired' $i ${i%%_1_*.fastq}_2_*.fastq; done is VelvetOptimiser.pl -t 12 -s 19 -v --d ~/comp_genomics/velvet_optimiser_jo/bb_17198wB1_Sample_2_assembly -f '-shortPaired -fastq bb_17198wB1_Sample_2_1_trimmed_prinseq.fastq b ...
written 1 hour ago by h.mon22k
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Answer: A: tools for global alignment
... Bowtie2 has an `--end-to-end` mode, read its [manual][1]. BBMap also is a global aligner. But I agree with https://www.biostars.org/u/20598/ when he says you concept of global alignment is not correct. [1]: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml ...
written 19 hours ago by h.mon22k
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Comment: C: Error in reago installation
... Did you try the error message suggestion? Did you try `conda info reago`? What is its output? Conda was experiencing disruptions due to internal updates yesterday, these should have been sorted out already. If you are lucky, the error you experienced was due to these updates, and if you try now it ...
written 1 day ago by h.mon22k
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Comment: C: Assembling ESTs and illumina reads
... Maybe you could assemble the Illumina reads and map them (or map the reads directly) and map the ESTs separately, then check for overlap. As an alternative, you could use [iAssembler][1] to join an Illumina Trinity assembly with the ESTs, but with so few ESTs, this would be too much time-consuming ...
written 1 day ago by h.mon22k
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Comment: C: Joining two files and KEEPING duplicates
... I don't want to over-react, but there is no reason for sarcasm. With the small example you provided, your command and https://www.biostars.org/u/30/ give identical results (except your results in space-delimited fields, and his, in tab-delimited fields). Maybe your problem is your files are not sor ...
written 1 day ago by h.mon22k
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Comment: C: interpreting fasta header
... Can you provide a little more background? Where did you get the file? Some co-worker / collaborator passed it to you? If so, ask them. Did you download it from some site / database / paper? Then please tell us where from. My guess is this is some unpublished internal / personal pipeline, and your ...
written 1 day ago by h.mon22k
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Comment: C: What is polygenic familiy phenomena?
... Hello tingtingxu0411! We believe that this post does not fit the main topic of this site. Not a bioinformatics question. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a ...
written 1 day ago by h.mon22k
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Answer: A: output path issue on Busco (python)
... > ERROR Please do not provide a full path in --out parameter, no slash. Use out_path in the config.ini file to specify the full path. It is a bit annoying you can't just give a path to `--out`. I would solve (in fact, it is what I do when I use BUSCO) the issue in a simpler manner than edi ...
written 1 day ago by h.mon22k
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... Minimap2 [paper][1] - a mapper to map them all. [1]: https://www.ncbi.nlm.nih.gov/m/pubmed/29750242/ ...
written 2 days ago by h.mon22k

Latest awards to h.mon

Scholar 1 day ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 4 days ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Scholar 4 days ago, created an answer that has been accepted. For A: BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
Scholar 4 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Scholar 4 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 5 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
Scholar 13 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 18 days ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Teacher 21 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
Scholar 21 days ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Scholar 21 days ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 23 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
Scholar 28 days ago, created an answer that has been accepted. For C: Identify insertions with IGV
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: FASTQ file format
Scholar 6 weeks ago, created an answer that has been accepted. For C: Identify insertions with IGV
Scholar 6 weeks ago, created an answer that has been accepted. For C: Identify insertions with IGV
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: FASTQ file format
Appreciated 6 weeks ago, created a post with more than 5 votes. For Benchmarking bioinformatics tools
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Converting BAM to Fastq - losing reads
Scholar 8 weeks ago, created an answer that has been accepted. For C: Identify insertions with IGV
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Scholar 8 weeks ago, created an answer that has been accepted. For C: Identify insertions with IGV
Scholar 8 weeks ago, created an answer that has been accepted. For C: Identify insertions with IGV

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