Moderator: Bastien Hervé

gravatar for Bastien Hervé
Bastien Hervé4.3k
Reputation:
4,260
Status:
Trusted
Location:
Limoges, CBRS, France
Last seen:
3 hours ago
Joined:
2 years, 4 months ago
Email:
b****************@orange.fr

Posts by Bastien Hervé

<prev • 768 results • page 1 of 77 • next >
0
votes
2
answers
123
views
2
answers
Comment: C: Is it possible to merge/combine three genome into one?
... Prokka would have help if you were looking at gene location on your genomes ...
written 14 days ago by Bastien Hervé4.3k
0
votes
2
answers
123
views
2
answers
Answer: A: Is it possible to merge/combine three genome into one?
... If I got you right you are trying to get unique parts of your 3 genomes to create a single one without redundancy. I do not think you can do that in a linear standard way. If you want to analyze your genes of your 28 genomes based on your 3 other genomes you can try [Prokka][1] If you want to alig ...
written 15 days ago by Bastien Hervé4.3k • updated 15 days ago by ATpoint18k
0
votes
0
answers
94
views
0
answers
Comment: C: RNA Seq, annotation, RNA Class
... You can have a look at [BiomaRt][1] from Ensembl [1]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 26 days ago by Bastien Hervé4.3k
0
votes
0
answers
151
views
0
answers
Comment: C: How to sort sam file using shell script?
... Why not using samtools ? You can take a look at `man sort` https://unix.stackexchange.com/questions/52762/trying-to-sort-on-two-fields-second-then-first ...
written 4 weeks ago by Bastien Hervé4.3k
3
votes
1
answer
125
views
1
answers
Answer: A: Fasta to FastQ with known qualities
... Hello https://www.biostars.org/u/55198/ Is it what you are looking for ? If you have solo line fasta this should work otherwise a python solution may be more suitable cat reads.fa | sed 's/>/@/g' | paste - - <(seq -w 1 $(grep -c ">" reads.fa) | xargs printf '+\n%.s') <(awk 'NR % 4 ...
written 4 weeks ago by Bastien Hervé4.3k
3
votes
2
answers
153
views
2
answers
Answer: C: What to pay attention when analyzing RNA-Seq samples from FFPE ?
... I would be interested to know if there are some criticals bias too ! A start in this Intro : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976456/ ...
written 5 weeks ago by Bastien Hervé4.3k
0
votes
1
answer
152
views
1
answers
Answer: A: Hisat2 splicesite file vs Tophat
... 1) No the phred33 option is use by default and will not filter out any reads based on their quality. It is a table cotation for score, on old sequencing machine phred64 table where used to report scores. Nowadays, sequencing machine use phred33 score table. I suggest you to not use this option at al ...
written 5 weeks ago by Bastien Hervé4.3k
1
vote
2
answers
130
views
2
answers
Comment: C: Tool to perform GSEA on mapped genes
... You can try this one : https://bioconductor.org/packages/release/bioc/vignettes/ReactomePA/inst/doc/ReactomePA.html ...
written 5 weeks ago by Bastien Hervé4.3k
0
votes
1
answer
152
views
1
answers
Answer: C: Applications of TPM normalisation
... You can use TPM to compare gene count in the same sample, but it is not the best way to go to compare genes across sample, prefer RLE or TMM method for example. This is one way to convert to TPM : https://support.bioconductor.org/p/91218/ Your function seems ok See also : https://youtu.be/TTUrtCY ...
written 6 weeks ago by Bastien Hervé4.3k
0
votes
2
answers
129
views
2
answers
Comment: C: Samtools: How to extract reads with MAPQ 0?
... > The "-q" parameter only filter out reads with MAPQ less then a specific value...therefore it is not working for me. What do you mean ? Option `-q` will extract reads with mapping quality above or equal the threshold. You cannot recover your 0 mapping quality this way. Even if you are able to ...
written 6 weeks ago by Bastien Hervé4.3k

Latest awards to Bastien Hervé

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 29 days ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Scholar 4 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Popular Question 6 weeks ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 8 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Scholar 8 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: RNA-seq, why normalize for library size?
Scholar 10 weeks ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Scholar 3 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Appreciated 3 months ago, created a post with more than 5 votes. For C: Python or R
Scholar 3 months ago, created an answer that has been accepted. 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
Popular Question 3 months ago, created a question with more than 1,000 views. For STAR index fail with gtf, works with gff3
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Need Help Writing Biopython to CSV
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: fastq parsing inefficiencies with python
Appreciated 4 months ago, created a post with more than 5 votes. For C: Python or R
Student 4 months ago, asked a question with at least 3 up-votes. For Apply Deseq2 size factor to aligned reads
Scholar 4 months ago, created an answer that has been accepted. For A: fastq parsing inefficiencies with python
Teacher 4 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1784 users visited in the last hour