Moderator: finswimmer

gravatar for finswimmer
finswimmer14k
Reputation:
13,720
Status:
Trusted
Location:
Germany
Last seen:
11 hours ago
Joined:
3 years, 10 months ago
Email:
f***********@gmail.com

Posts by finswimmer

<prev • 1,651 results • page 1 of 166 • next >
0
votes
2
answers
138
views
2
answers
Comment: C: how to unique a file row-wise?
... Hello https://www.biostars.org/u/21479/, how is this question related to bioinformatics? Is the order of the numbers per row in the output important? If so, how is the relationship to the input? fin swimmer ...
written 8 days ago by finswimmer14k
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Confused about how to generate a consensus sequence after bwa
... Hello https://www.biostars.org/u/25073/, > But I can't use bcftools consensus because it will not generate a consensus sequence from a FASTA reference containing multiple sequences. can you add more information what you mean by this and how it looks like? A fasta file can contain multiple seq ...
written 8 days ago by finswimmer14k
0
votes
2
answers
163
views
2
answers
Answer: A: bcftools missing most indels in variant calling
... Interesting, I don't know why `bcftools` is missing that much variants here. I was able to reproduce it. In my experience [freebayes](https://github.com/freebayes/freebayes) is the better choice if you are mainly interested in indels. In a short test it finds variants in 400 positions. ...
written 27 days ago by finswimmer14k
2
votes
2
answers
226
views
2
answers
Answer: C: Sanger sequencing Result: Difference between forward and reverse DNA strands
... The second sequence is the reverse complement sequence of the first one. So the variant 227G>A is 309 C>T in the second. And 245C>G is 290 G>C in the second. Looks all good to me. ...
written 4 weeks ago by finswimmer14k
0
votes
0
answers
181
views
0
answers
Comment: C: how to parse a genome "start point to end point" and find what genes inside?
... Hello https://www.biostars.org/u/79298/, you should show us, how your data looks like exactly. Otherwise we can just guess. fin swimmer ...
written 5 weeks ago by finswimmer14k
0
votes
1
answer
124
views
1
answers
Answer: A: Freebayes - not detecting some ALT alleles
... Hello, AFAIK `freebayes` assumes by default, that your sample is diploid. So it will never give you more than two alleles for a specific position. Of course there are some parameter you can use, to get more information. `freebayes --help` is mentioning a combination of parameters that looks promis ...
written 5 weeks ago by finswimmer14k
3
votes
3
answers
215
views
3
answers
Answer: C: Best ubuntu version for bioinformatics?
... The choice of the distribution isn't that important. Choose any more or less current one. To install and manage your bioinformatics tools use [conda](https://docs.conda.io/en/latest/miniconda.html) with the [bioconda channel](https://bioconda.github.io/user/install.html) activated. The first part of ...
written 5 weeks ago by finswimmer14k
0
votes
0
answers
152
views
0
answers
Comment: C: convert TCGA hg38 maf to hg 19 maf
... Hello https://www.biostars.org/u/49704/, why do you want do convert to a reference genome that is outdated for 7 years now? fin swimmer ...
written 12 weeks ago by finswimmer14k
0
votes
0
answers
138
views
0
answers
Comment: C: FASTA file header
... > However, after aligning to reference, vcf ID from the header disappears, Can you show an example of your expected output? ...
written 12 weeks ago by finswimmer14k
1
vote
2
answers
208
views
2
answers
Answer: A: I have more reads after extracting those that are mapped...
... Hello, according to [this docs](https://gslweb.discoveryls.com/information/software/bam2fastq) `bam2fastq` assumes that each read is aligned only once in the bam file. This is rarely the case. There are always a bunch of reads that are mapped multiple times. So I guess `bam2fastq` will extract the ...
written 12 weeks ago by finswimmer14k

Latest awards to finswimmer

Popular Question 13 days ago, created a question with more than 1,000 views. For GC Bias Correction
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 4 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Epic Question 5 months ago, created a question with more than 10,000 views. For Creating workflows with snakemake and conda
Great Question 5 months ago, created a question with more than 5,000 views. For Which human reference genome should I use?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information
Appreciated 6 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Popular Question 6 months ago, created a question with more than 1,000 views. For Which human reference genome should I use?
Appreciated 6 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 7 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 8 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Student 8 months ago, asked a question with at least 3 up-votes. For Difference between | and || in filtering expressions by bcftools
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 8 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Merging FASTA files
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 9 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1858 users visited in the last hour
_