Moderator: Dan D

gravatar for Dan D
Dan D5.9k
Reputation:
5,940
Status:
Trusted
Location:
Tennessee
Website:
http://automationdan.com/
Last seen:
17 hours ago
Joined:
5 years, 2 months ago
Email:
d*******@gmail.com

Docendo discimus.

Posts by Dan D

<prev • 607 results • page 1 of 61 • next >
3
votes
1
answer
324
views
1
answers
Answer: A: How to extract whole gene sequence with 5' and 3' UTR from genome
... ##Step 1: Download and index the genome with samtools faidx: samtools faidx [radish.fa] ## Step 2: Extract the region of interest: samtools faidx [radish.fa] [contig_name:start_pos-end_pos] The result will be printed to STDOUT. ...
written 4 months ago by Dan D5.9k
0
votes
0
answers
23
views
0
answers
Comment: C: regular expression on Notepad+++
... I can't help it, I'm compelled to answer the question anyway. Find what: ^\s\d\s Replace with: To be clear: don't put anything in the "replace with" field. That should work if I'm understanding your query correctly. ...
written 4 months ago by Dan D5.9k
0
votes
0
answers
23
views
0
answers
Comment: C: regular expression on Notepad+++
... Hello chenmengutd! We believe that this post does not fit the main topic of this site. This is not related to bioinformatics 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 ...
written 4 months ago by Dan D5.9k
2
votes
1
answer
215
views
1
answers
Answer: A: How can I retrieve the info to recreate this figure for my own data?
... Excel from the 2010 edition onward can accomplish something like your figure pretty easily. There's also [SigmaPlot][1], which is what I used before I became proficient with d3.js and matplotlib. This figure actually resembles a standard matplotlib product to me. [Tableau][2] is great too, but p ...
written 4 months ago by Dan D5.9k
2
votes
0
answers
390
views
0
answers
Comment: C: Demultiplex fastq files in which barcodes and primers are already removed
... Assuming this is the case (which hopefully it is), which tool will help him do what he needs? Fill in the blank: BB_________ ...
written 4 months ago by Dan D5.9k
0
votes
0
answers
220
views
0
answers
Tool: LabwareJS: Represent Microplates and Flowcells in SVG
... I know from previous questions that a lot of us get roped into doing LIMS work, which sometimes directly involves bioinformatics and other times is just tangential. There are also situations where we need to make interfaces to existing tools. Anyway, I don't see much out there for rendering labware ...
lims tool svg written 5 months ago by Dan D5.9k
1
vote
0
answers
390
views
0
answers
Comment: C: Demultiplex fastq files in which barcodes and primers are already removed
... Can you please `head` the converted FASTQ file so we can get a basic overview of its structure? ...
written 5 months ago by Dan D5.9k
3
votes
1
answer
267
views
1
answers
Answer: A: Piping a bam file to samtools calmd
... In bash you need to use `-` to specify that the input is coming from a pipe. You should also add the `-S` parameter to specify that the input is SAM (or follow the suggestion of @swbarnes2 and output BAM from `view` instead): samtools view -h -F 0x10 | samtools calmd -S - | samtools view -bS ...
written 5 months ago by Dan D5.9k
1
vote
0
answers
259
views
0
answers
Comment: C: How can I open .fusion file for fusion detection from RNA-seq analysis
... Try the following on the command line: less [my_file.fusions] If you see human-readable output, that means you should be able to open the file in a normal text editor. If you see regular spacing or delimiters in the body of the text, you can probably open and view it with spreadsheets software. ...
written 5 months ago by Dan D5.9k
0
votes
0
answers
151
views
0
answers
Comment: C: Confusion regarding Trinity analyze_diff_expr.pl
... Hello phuongbigbig! Questions similar to yours can already be found at: Confusion regarding Trinity analyze_diff_expr.pl We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be ...
written 5 months ago by Dan D5.9k

Latest awards to Dan D

Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Scholar 5 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For C: I want to re-open the old debate: python or perl ?
Popular Question 10 months ago, created a question with more than 1,000 views. For Unable To Replicate Splice Junction In Tophat
Scholar 12 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Bwa or bowtie for mapping mulitple genomes
Popular Question 14 months ago, created a question with more than 1,000 views. For Unable To Replicate Splice Junction In Tophat
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Getting Started With Ngs Analysis For Modeling Guy
Scholar 14 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Getting Started With Ngs Analysis For Modeling Guy
Scholar 15 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Appreciated 15 months ago, created a post with more than 5 votes. For A: what is in the fasta.fai
Scholar 15 months ago, created an answer that has been accepted. For A: what is in the fasta.fai
Scholar 15 months ago, created an answer that has been accepted. For A: Bwa or bowtie for mapping mulitple genomes
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Looking for opinions on PhD programs in Genetics and Genomics/Bioinformatics
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Getting Started With Ngs Analysis For Modeling Guy
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Getting Started With Ngs Analysis For Modeling Guy
Popular Question 16 months ago, created a question with more than 1,000 views. For Unable To Replicate Splice Junction In Tophat
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: How to plot coverage and depth statistics of a bam file
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: I loaded a BAM (RNA-seq) file into IGV but cant see anything!
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: I loaded a BAM (RNA-seq) file into IGV but cant see anything!
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: I loaded a BAM (RNA-seq) file into IGV but cant see anything!

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1302 users visited in the last hour