User: finswimmer

gravatar for finswimmer
finswimmer1.4k
Reputation:
1,390
Status:
Trusted
Location:
Germany
Last seen:
26 minutes ago
Joined:
1 year, 1 month ago
Email:
f***********@gmail.com

Posts by finswimmer

<prev • 249 results • page 1 of 25 • next >
0
votes
0
answers
56
views
0
answers
Comment: C: Needleman Wunsch algorithm coding in python for global alignment
... Hello hbleed121, what kind of trouble are your facing? Please be more specific. Or is it just a general coding question about how you can make your code faster, shorter, more beautiful, .... ? fin swimmer ...
written 1 day ago by finswimmer1.4k
0
votes
2
answers
101
views
2
answers
Comment: C: How to extract forward and reverse primer coordinates for soft clipping?
... Hello bioinfo89, the idea was using bbduk to remove your primer sequences from your reads and not just the adapters. So if you already removed your adapters trimm your data a second time using bbduk and provide a "adapter file" containing the sequences of your primers. fin swimmer ...
written 2 days ago by finswimmer1.4k
0
votes
2
answers
101
views
2
answers
Comment: C: How to extract forward and reverse primer coordinates for soft clipping?
... Hello bioinfo89, as genomax said it's a better idea to trim your data using the adapter trimming function from [bbduk][1]. fin swimmer [1]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ...
written 3 days ago by finswimmer1.4k
0
votes
3
answers
76
views
3
answers
Answer: A: Filter variants in vcf file according to genotype of particular samples?
... Hello arsala521, you can filter with [SnpSift][1]. Especially have a look at the part "Available operands and functions". fin swimmer [1]: http://snpeff.sourceforge.net/SnpSift.html#filter ...
written 3 days ago by finswimmer1.4k
3
votes
1
answer
75
views
1
answers
Answer: A: SNP/indel annotation in Arabidopsis
... Hello, have a look at [snpEff][1]. Your list of SNP/indel have to be in vcf or bed format. fin swimmer [1]: http://snpeff.sourceforge.net/SnpEff_manual.html ...
written 3 days ago by finswimmer1.4k
0
votes
0
answers
90
views
0
answers
Comment: C: Picard Mark Duplicates
... > Regarding the soft clip bases, I don't think soft clipped bases has to > do with this thing because the position 88015806 in the above example > is the position start of the alignment and not the soft clipped bases. You're right. The alignment starts with the first not soft clipped base. ...
written 4 days ago by finswimmer1.4k
0
votes
0
answers
90
views
0
answers
Comment: C: Picard Mark Duplicates
... > The MarkDuplicates tool works by comparing sequences in the 5 prime > positions of both reads and read-pairs in a SAM/BAM file. Oh, have they changed their algorhithm or just the explanation? I have in mind, that picard MarkDuplicate doesn't compare any sequence, but look at the most 5' map ...
written 4 days ago by finswimmer1.4k
4
votes
3
answers
211
views
3
answers
Answer: A: SNPs in 1000 genome project
... Hello Javad, without a little work you will not reach your goal. The most difficult part here is, to clarify who said what is an exon? UCSC, NCBI, Ensembl,...? And do you want just coding exons or all? Let's assume you like all exons defined by NCBI. 1. Go to [UCSC Table browser][1] 2. Choose hg ...
written 5 days ago by finswimmer1.4k
1
vote
2
answers
177
views
2
answers
Answer: A: make fasta sequence which is multiple of three
... Beside the correct question from Ram why you want to do this, here is a python solution: from Bio import SeqIO original_file = "./original.fasta" extended_file = "./extended.fasta" with open(original_file) as original, open(extended_file, 'w') as extended: records ...
written 5 days ago by finswimmer1.4k
1
vote
0
answers
102
views
0
answers
Comment: C: phasing vcf file
... Hello, have a look into the [manual][1]. The Stack needs more memory. You can set the size with the `–Xss` parameter. For example use `–Xss5m` to set the stack size to 5Mb. Please use the code button to mark code. It is better to read. And if you found a post helpful please upvote it. fin swimme ...
written 5 days ago by finswimmer1.4k

Latest awards to finswimmer

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 3 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 3 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 6 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 12 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 15 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Guru 26 days ago, received more than 100 upvotes.
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For A: sam file error
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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 6 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Why not merging?
Appreciated 4 months ago, created a post with more than 5 votes. For Why not merging?
Scholar 4 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 5 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1036 users visited in the last hour