Moderator: Asaf

gravatar for Asaf
Asaf4.1k
Reputation:
4,140
Status:
Trusted
Location:
Israel
Scholar ID:
Google Scholar Page
Last seen:
2 days, 12 hours ago
Joined:
6 years, 3 months ago
Email:
a*****@gmail.com

Posts by Asaf

<prev • 459 results • page 1 of 46 • next >
0
votes
1
answer
164
views
1
answers
Comment: C: trim adaptors RNA-seq
... I usually ignore over-represented sequences, especially in RNAseq. It depends a lot on the library preparation and in such low levels it's not a concern. You can test the FastQC on the R2 reads, they should have the same adapter sequence. run cutadapt as you intended (isn't it -a for forward and -A ...
written 8 days ago by Asaf4.1k
1
vote
1
answer
164
views
1
answers
Comment: C: trim adaptors RNA-seq
... They do match. There is the initial A from the ligation and the end of the sequence you found is not present in the adapter sequence of FastQC. Go with the FastQC sequence ...
written 8 days ago by Asaf4.1k
0
votes
0
answers
115
views
0
answers
Comment: C: change a mitochondria genome genebank file to a fasta file including multiple fa
... If you have the RefSeq accession number you can probably download it as a FASTA file ...
written 16 days ago by Asaf4.1k
0
votes
0
answers
134
views
0
answers
Comment: C: RNA-seq compare FPKM's or fold change of different organisms
... Comparing read count between organisms is not recommended. Comparing fold-change, however, sounds like a good idea if you could find similar comparisons. ...
written 16 days ago by Asaf4.1k
0
votes
0
answers
132
views
0
answers
Comment: C: Blastn: Blast short reads against genomes and retain only good hits
... you can add alignment length to output and filter according to it (using awk). ...
written 16 days ago by Asaf4.1k
0
votes
0
answers
284
views
0
answers
Comment: C: Best way to address different batches of RNA-seq
... What was different between the two batches? In addition, as said above you shouldn't use RPKM, use statistics as in DESeq2 ...
written 11 weeks ago by Asaf4.1k
0
votes
1
answer
168
views
1
answers
Answer: A: Gene abundance profile from metagenomics data
... I'm not aware of such a tool. You can try and classify your genes using interpro domains, MetaCyc/KEGG orthology groups etc. Depending on your depth of sequencing and sample complexity I would consider reference-based counting (i.e. mapping the reads to a reference using blastx) instead of assembly ...
written 11 weeks ago by Asaf4.1k
0
votes
0
answers
226
views
0
answers
Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... DESeq2 normalization process assumes that most of the entities are the same in all of the samples. If you think that this assumption applies then you're good to go with DESeq2, you can go forward and do the entire analysis with it. If, however, this is not the case and the population is completely d ...
written 3 months ago by Asaf4.1k
0
votes
0
answers
226
views
0
answers
Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... If you have a table with read counts then DESeq2 should work, the main issue here is what reference to use. ...
written 3 months ago by Asaf4.1k
0
votes
1
answer
201
views
1
answers
Comment: C: Identifying paralogs using phylogenetic tree
... You might want to take a look at: https://www.nature.com/nature/journal/v449/n7158/full/nature06107.html They did this for fungi and were able to track down paralogs, especially after the whole genome duplication event. ...
written 3 months ago by Asaf4.1k

Latest awards to Asaf

Appreciated 3 months ago, created a post with more than 5 votes. For A: How To Mark Specific Species On The Tree Of Life?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: What to do after an genome assembly?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 4 months ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Popular Question 5 months ago, created a question with more than 1,000 views. For Getting transcripts from BAM file with gene names
Scholar 6 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How To Mark Specific Species On The Tree Of Life?
Popular Question 9 months ago, created a question with more than 1,000 views. For Counting reads for gene in bacterial genomes
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Popular Question 11 months ago, created a question with more than 1,000 views. For What Do You Waste Your Time On
Scholar 11 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Scholar 12 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Scholar 13 months ago, created an answer that has been accepted. For A: What are the "Coding", "Maximal" and "Two templates" options for megablast?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms
Great Question 16 months ago, created a question with more than 5,000 views. For What Do You Waste Your Time On
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Find Enriched Function In Go Terms

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1358 users visited in the last hour