Moderator: Bastien Hervé

gravatar for Bastien Hervé
Bastien Hervé3.3k
Reputation:
3,260
Status:
Trusted
Location:
Limoges, CBRS, France
Last seen:
6 hours ago
Joined:
2 years ago
Email:
b****************@orange.fr

Posts by Bastien Hervé

<prev • 639 results • page 1 of 64 • next >
0
votes
0
answers
66
views
0
answers
Comment: C: Principal/Sr Principal Scientist, bioinformatics
... Please, update your link, it is not valid ...
written 6 hours ago by Bastien Hervé3.3k
0
votes
1
answer
68
views
1
answers
Comment: C: A large list of chromossome
... I can suggest you to take a look at [karyoploteR][1]. I use it a lot to display information on chromosomes. There is a `Plot SNP array raw data` tutorial that produces a result really close to what you want. [1]: https://bernatgel.github.io/karyoploter_tutorial//Examples/SNPArray/SNPArray.html ...
written 16 hours ago by Bastien Hervé3.3k
1
vote
1
answer
72
views
1
answers
Comment: C: automatically create index files from output in bcftools
... If there is an other command called `bcftools index` why would you want to use an option to index your file in `bcftools view` ? If you want a single command line to do both you can : /share/apps/genomics/bcftools-1.9/bin/bcftools view -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz ...
written 1 day ago by Bastien Hervé3.3k
3
votes
1
answer
176
views
1
answers
Answer: A: ChipSeq using MACS2 - option to not call peaks with only few reads ?
... As there is no perfect answer but only homemade solutions, here is mine according to what I'm interested in. So, as suggested by https://www.biostars.org/u/25721/, I need to find a "number of mapped reads on a given area" threshold to limit the call of false positive peaks (bin with high fold change ...
written 1 day ago by Bastien Hervé3.3k
0
votes
1
answer
68
views
1
answers
Comment: C: A large list of chromossome
... Please give us a look of the inside of `felis_catus_chrom` variable ...
written 2 days ago by Bastien Hervé3.3k
3
votes
1
answer
60
views
1
answers
Comment: C: combining overlapping vcf's into one
... You can take a look at `vcf-merge` in [vcf-tools][1] [1]: http://vcftools.sourceforge.net/perl_module.html ...
written 2 days ago by Bastien Hervé3.3k
1
vote
1
answer
106
views
1
answers
Comment: C: Reference geneome of wheat for Bowtie
... Hello https://www.biostars.org/u/52498/, This is a `question` not a `tool`, Tool section is used to highlight a new software. Could you please correct some misspelling like : >reads from fastaq file fasta or fastq ? >.fast fasta or fastq ? Take a look here for reference genome and annot ...
written 2 days ago by Bastien Hervé3.3k
0
votes
1
answer
74
views
1
answers
Comment: C: how to locate genes coding on the reference genome
... Like a classic aligner BWA/Bowtie2 or do you want to align your sequences on the 6 genomes at once ? ...
written 3 days ago by Bastien Hervé3.3k
1
vote
1
answer
85
views
1
answers
Comment: C: Detecting Klinefelter from genomic files
... Could have be the number of mapped read per chromosome / chromosome length, or something similar. Anyway Pierre' answer is much more advance, mine is just theorical ! ...
written 3 days ago by Bastien Hervé3.3k
1
vote
1
answer
85
views
1
answers
Comment: C: Detecting Klinefelter from genomic files
... Is that the XXY disease ? My guess is, If you have an homogeneous depth over your no sexual chromosome and that you get twice the amount of reads on chrX the subject got the disease. ...
written 3 days ago by Bastien Hervé3.3k

Latest awards to Bastien Hervé

Commentator 1 day ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Appreciated 8 days ago, created a post with more than 5 votes. For C: Python or R
Student 9 days ago, asked a question with at least 3 up-votes. For Apply Deseq2 size factor to aligned reads
Scholar 15 days ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Commentator 17 days ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Popular Question 25 days ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Scholar 8 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 9 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Python or R
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Scholar 11 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Appreciated 11 weeks ago, created a post with more than 5 votes. For C: Python or R
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Student 3 months ago, asked a question with at least 3 up-votes. For Apply Deseq2 size factor to aligned reads
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Scholar 4 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Voter 4 months ago, voted more than 100 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 796 users visited in the last hour