Moderator: Damian Kao
Damian Kao ♦ 15k
- Reputation:
- 15,420
- Status:
- Trusted
- Location:
- USA
- Website:
- http://blog.nextgeneti...
- Last seen:
- 3 hours ago
- Joined:
- 8 years, 8 months ago
- Email:
- d*********@gmail.com
Bioinformatician at Janelia Research Campus.
Posts by Damian Kao
<prev
• 912 results •
page 1 of 92 •
next >
0
votes
0
answers
301
views
0
answers
... My recommendation is to not over-optimize unless this is a personal project for learning purposes.
There are three main considerations here all related to scale:
1. How many concurrent users do you expect to be using this database?
2. Is this pre-dominantly a read-only database where users query ...
written 12 months ago by
Damian Kao ♦ 15k
0
votes
1
answer
503
views
1
answers
... Try setting --outFilterMatchNmin to 20 to see if you can get more mapping. However, that means it only requires 20 bases to map, which is pretty low. ...
written 14 months ago by
Damian Kao ♦ 15k
2
votes
2
answers
758
views
2
answers
... Technically, RPK values do not violate assumptions of TMM.
TMM is just a technique that tries to find the non-DE portion of the expression distribution by very liberally trimming off outliers. It doesn't matter what kind of expression units you are using.
However, RPK values do violate assumptio ...
written 14 months ago by
Damian Kao ♦ 15k
3
votes
1
answer
626
views
1
answers
Answer:
A: Trimmomatic output file Issue
... It looks like you are not specifying an output file for the -trimlog parameter. So it thinks your `output_forward_paired.fq.gz` is an input.
I hope you still can still redownload `sample1_R1_001.fastq.gz`, because it might have been overwritten. ...
written 14 months ago by
Damian Kao ♦ 15k
1
vote
8
answers
1.1k
views
8
answers
... Takes in fasta file and a second parameter for homopolymer length.
It streams through each line to find homopolymers. Outputs chromosome, start, end, homopolymer base, length of homopolymer.
I tested it out on this fasta file:
>A
AGTCAAAA
GGGGTTTTCCCC
>B
AGTCCCCCTTTTAAA ...
written 15 months ago by
Damian Kao ♦ 15k
5
votes
4
answers
747
views
4
answers
... You have a .csv file with chromosome, start, end coordinates. You can change that into a .bed file pretty easily. Same with your SNP csv file.
Convert those csv files to bed and then use bedtools intersect. ...
written 15 months ago by
Damian Kao ♦ 15k
0
votes
0
answers
688
views
0
answers
... Yeah that could be it. You can check this by looking at the insert size distribution of your PE reads. See if it is smaller than 2 * average read length. The 9th column of your .sam/.bam should be the insert size. ...
written 16 months ago by
Damian Kao ♦ 15k
2
votes
0
answers
669
views
0
answers
... I am not sure what program you are using to generate the .vcfs. But you should look into the manual of the program and see if it outputs depths using the format fields in the vcf. For example, you have "DP" field in your vcf that shows the depth of the individual samples. Perhaps one of the other f ...
written 16 months ago by
Damian Kao ♦ 15k
0
votes
0
answers
669
views
0
answers
... Can you post a couple of lines of your vcf file? ...
written 16 months ago by
Damian Kao ♦ 15k
5
votes
1
answer
578
views
1
answers
... There is a -L flag that you can use with samtools to output alignments overlapping intervals defined by a .bed file. That's probably your best option. You'll have to convert your exons.txt to a bed file. ...
written 16 months ago by
Damian Kao ♦ 15k
Latest awards to Damian Kao
Great Question
4 weeks ago,
created a question with more than 5,000 views.
For Chip-seq analysis with input and spike-in
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For Abyss unitigs filtering
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Great Question
3 months ago,
created a question with more than 5,000 views.
For Encode Commentary From Dan Graur
Great Question
4 months ago,
created a question with more than 5,000 views.
For Encode Commentary From Dan Graur
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Interpreting Trinity components
Popular Question
11 months ago,
created a question with more than 1,000 views.
For segment duplication vs heterozygosity
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Scholar
14 months ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Scholar
14 months ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Scholar
16 months ago,
created an answer that has been accepted.
For C: What's the correct way to withdraw a published database/server ?
Appreciated
16 months ago,
created a post with more than 5 votes.
For A: A Farewell To Bioinformatics
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Good Answer
17 months ago,
created an answer that was upvoted at least 5 times.
For A: A Farewell To Bioinformatics
Commentator
18 months ago,
created a comment with at least 3 up-votes.
For C: Shall We Go Back To Stackexchange?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For deseq2 user defined size factors
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1358 users visited in the last hour