User: Aremkh

gravatar for Aremkh
Aremkh20
Reputation:
20
Status:
New User
Location:
Last seen:
5 hours ago
Joined:
4 years, 10 months ago
Email:
e********@gmail.com

Posts by Aremkh

<prev • 22 results • page 1 of 3 • next >
0
votes
1
answer
145
views
1
answers
Answer: A: Linkage_pruning in BCFtools+prune:phased or unphased VCF input file?
... In case you have the same question, please refer to the answer at: https://github.com/samtools/bcftools/issues/1237 Briefly, unphased data are suitable. ...
written 4 weeks ago by Aremkh20
0
votes
1
answer
145
views
1
answer
Linkage_pruning in BCFtools+prune:phased or unphased VCF input file?
... Dear Colleagues, I am wondering if the LD pruning method applied in bcftools+prune plugin required the input VCF file to be phased or alternatively unphased VCF files still can be used? Many thanks in advance -l, --max-LD R2 remove sites with r2 bigger than R2 within the -w window ...
haplotype_phasing bcftools+prune snp written 9 weeks ago by Aremkh20
0
votes
1
answer
137
views
1
answers
Comment: C: BWA_MEM SHORT READS
... Many thanks for your advice! ...
written 4 months ago by Aremkh20
4
votes
1
answer
137
views
1
answer
BWA_MEM SHORT READS
... Dear colleagues, I have used BWA-MEM to algin single end 50 bp reads against scaffolds. The performance is far superior compared to other aligners. However, my question is that given the recommended minimum 70 bp read length in the paper, does the recommended read length only affect the computation ...
bwa_mem read length written 4 months ago by Aremkh20
0
votes
1
answer
176
views
1
answers
Comment: C: abyss assembly and bubbles
... Thanks Lauren ! It was really helpful! Cheers ...
written 5 months ago by Aremkh20
0
votes
1
answer
176
views
1
answer
abyss assembly and bubbles
... Dear Colleagues, We are assembling an insect genome from a large pool of different individuals. As an artefact of pool sequencing, we have a large number of polymorphisms that end up as bubbles in the assembly graph. I am wondering if any of developers and/or experienced users recommend any speci ...
assembly abyss written 5 months ago by Aremkh20 • updated 5 months ago by lauren.e.coombe0
0
votes
1
answer
1.3k
views
1
answers
Comment: C: recommendations for DeNovo assembly of short reads
... Thanks Asaf ! It is for mammalian genome (2n)! ...
written 2.6 years ago by Aremkh20
2
votes
1
answer
1.3k
views
1
answer
recommendations for DeNovo assembly of short reads
... Dear Colleagues , I have been away from the field for a while. I am wondering if you have any recommendations regarding a package to assemble de novo Illumina 2X250 reads in to contigues/scaffolds ? In my time Velvet was very popular. There are probably new tools around that I am unaware of them. ...
software assembly shortreads denovo written 2.6 years ago by Aremkh20 • updated 2.5 years ago by h.mon30k
0
votes
0
answers
520
views
0
answers
Comment: C: massive multiple alignment suggestion
... Hi there, Thanks for the replay. Yes the goal is ultimately assigning SNPs. Sorry for silly question: I really don't have much idea about reducing redundancy !javascript:document.forms["comment-form"].submit() ...
written 2.6 years ago by Aremkh20
0
votes
0
answers
520
views
0
answers
massive multiple alignment suggestion
... Dear Colleagues, I have a set of massive random shot gun sequencing data from few organism without reference genome. I would like to ask your kind expert suggestions if you know a pipeline for aligning all against all for finding "stacks" of aligned homologous reads. They have been generated randoml ...
software sequence alignement snp written 2.6 years ago by Aremkh20

Latest awards to Aremkh

Scholar 4 weeks ago, created an answer that has been accepted. For A: Linkage_pruning in BCFtools+prune:phased or unphased VCF input file?
Popular Question 3 months ago, created a question with more than 1,000 views. For Go Term enrichment
Popular Question 4 months ago, created a question with more than 1,000 views. For Go Term enrichment
Popular Question 18 months ago, created a question with more than 1,000 views. For Go Term enrichment
Popular Question 18 months ago, created a question with more than 1,000 views. For GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
Popular Question 18 months ago, created a question with more than 1,000 views. For SNPEFF for de novo transcriptome annotation
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
Popular Question 3.2 years ago, created a question with more than 1,000 views. For GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 697 users visited in the last hour