Moderator: swbarnes2
swbarnes2 ♦ 2.8k
- Reputation:
- 2,770
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 22 hours ago
- Joined:
- 5 years, 5 months ago
- Email:
- s********@gmail.com
about me
Posts by swbarnes2
<prev
• 244 results •
page 1 of 25 •
next >
0
votes
1
answer
261
views
1
answers
... samtools fasta will not generate a reference fasta. It turns each read from a one line sam format into two line fasta format. samtools.pl should have pileup2fq, that is closer to what you want. ...
written 5 weeks ago by
swbarnes2 ♦ 2.8k
0
votes
2
answers
201
views
2
answers
Answer:
A: align spike in database
... Make a new reference file which includes the spike-in sequences. Reindex that genome with Bowtie, realign. ...
written 8 weeks ago by
swbarnes2 ♦ 2.8k
0
votes
3
answers
3.4k
views
3
answers
... My version of samtools 1.4 doesn't have vcfutils.pl. It does have samtools.pl, which has pileup2fq, so you might want to try that.
You can make your own pileup2fa pretty easily, by editing the samtools.pl script. perl scripts are plain texts, so you can look at them easily.
Find the the code b ...
written 9 weeks ago by
swbarnes2 ♦ 2.8k
3
votes
1
answer
199
views
1
answers
Answer:
A: FastQ format (\n)
... If you are asking if it's okay to just concatenate fastq files together, yes, you can do that. You can also just 'cat' fastq.gz files together. It all works fine. No need to strip an EOF character off prior to concatenating. ...
written 10 weeks ago by
swbarnes2 ♦ 2.8k
1
vote
1
answer
196
views
1
answers
... Quick and dirty approach is to align just to virus, but you might get human reads that would better align to human genome falsely aligning to your viral genome, because that' all you gave it to match to. Better is to align to viral and human genome together. The alignment will be more accurate lik ...
written 10 weeks ago by
swbarnes2 ♦ 2.8k
0
votes
2
answers
347
views
2
answers
... If you know the coordinates of the gene, you could use awk or bedtools to get all mutations in a specific genomic interval. ...
written 5 months ago by
swbarnes2 ♦ 2.8k
2
votes
1
answer
292
views
1
answers
... Go to the fasta that you downloaded for use with PASH, change all the spaces in the reference names to underscores. Remake the genome index, realign. ...
written 5 months ago by
swbarnes2 ♦ 2.8k
2
votes
1
answer
292
views
1
answers
... I wonder if having spaces in your references sequence names is the problem; Maybe Bowtie is okay with them, but PASH is not. I'd fix that, and realign. ...
written 5 months ago by
swbarnes2 ♦ 2.8k
0
votes
0
answers
490
views
0
answers
Comment:
C: Meta-analysis of RNA-seq Data
... If you have no biological replicates, your dataset doesn't actually tell you very much. ...
written 6 months ago by
swbarnes2 ♦ 2.8k
0
votes
3
answers
302
views
3
answers
... Simple not-very-clever solution...use grep or something to split out the files by chromosome, sort those individually, then cat them back together (with the orignal headers) ...
written 6 months ago by
swbarnes2 ♦ 2.8k
Latest awards to swbarnes2
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To B
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: Blast: Homology Or Similarity?
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: What Does Color Space And Nucleotide Space Mean (Data, Reference Genome Etc.) ?
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Appreciated
21 months ago,
created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
Teacher
3.1 years ago,
created an answer with at least 3 up-votes.
For A: Which Is The Best Way For Filtering A Vcf File For Only Variation Sites?
Good Answer
3.2 years ago,
created an answer that was upvoted at least 5 times.
For A: How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
Good Answer
3.2 years ago,
created an answer that was upvoted at least 5 times.
For A: Blast: Homology Or Similarity?
Appreciated
3.3 years ago,
created a post with more than 5 votes.
For A: Blast: Homology Or Similarity?
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: Question: Can Anyone Suggest Me A Script To Do A Gene Name Rearrangement
Supporter
3.4 years ago,
voted at least 25 times.
Centurion
3.4 years ago,
created 100 posts.
Guru
3.4 years ago,
received more than 100 upvotes.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1474 users visited in the last hour