User: al-ash
al-ash • 60
- Reputation:
- 60
- Status:
- Trusted
- Location:
- Japan/Okinawa/OIST
- Last seen:
- 10 hours ago
- Joined:
- 3 years, 6 months ago
- Email:
- b*********@gmail.com
Posts by al-ash
<prev
• 59 results •
page 1 of 6 •
next >
0
votes
2
answers
738
views
2
answers
... Please show also the headers of the alignments which "are fine" to see if the problem is header length.
I had this error when my input phylip file had between sequence name and sequence tab instead of two spaces. Replacing the tab by two spaces (e.g. in bash via sed 's/\t/ /') fixed the problem - ...
written 2 days ago by
al-ash • 60
1
vote
2
answers
2.5k
views
2
answers
... Since this is one of the top hits when searching online for manual editing of multiple alignments, I'd like to reopen this topic to hopefully collect suggestions for some more tools than JalView for visual inspection and editing of multiple sequence alignments.
One common task is identification of ...
written 18 days ago by
al-ash • 60
0
votes
4
answers
790
views
4
answers
... I ended up with the following command line solution using clustal omega which converts distance matrix to percent identity matrix:
clustalo-1.2.4-Ubuntu-x86_64 --full --percent-id --distmat-out=output.distmat -i input.aa.fa ...
written 4 weeks ago by
al-ash • 60
0
votes
1
answer
759
views
1
answers
... In the example, they use `2> assemble.log` to redirect stderror to a file. In your original command you made a mistake by typing a space between `2` and `>`. That's why removing 2 helped. Alternatively, removing the space should fix this as well. ...
written 10 weeks ago by
al-ash • 60
1
vote
1
answer
235
views
1
answer
... I was using tanglegram() function from a great R package dendextend to draw comparison of phylogenetic trees. However, it requires to have identical set of tip labels in both trees and gives following error when presented with two trees with not identical set of tip labels:
Error in match_order ...
1
vote
1
answer
392
views
1
answer
... I'm using Trimmomatic/0.33 to proces my raw Illumina reads.
I've seen some adapter contamination with FASTQC so I first run Trimmomatic as follows:
java -jar trimmomatic-0.33.jar PE R1.fastq.gz R2.fastq.gz PR1.fastq.gz UPR1.fastq.gz PR2.fastq.gz UPR2.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:1 ...
written 6 months ago by
al-ash • 60
• updated
5 months ago by
finswimmer ♦ 7.7k
0
votes
3
answers
13k
views
3
answers
... (typo: should be -max_target_seqs instead of -max_target_seqns) ...
written 8 months ago by
al-ash • 60
0
votes
2
answers
2.5k
views
2
answers
... Did you reach any conclusion? If so, please share - this question is still missing an answer supported by some experience/evidence/literature reference. ...
written 8 months ago by
al-ash • 60
1
vote
1
answer
1.3k
views
1
answers
... Concerning your 1st question (dS for each branch) - you can find it among the large amount of output information in the outfile (ENSGT00790000122969.mlc in your case) in a tabular form (in section labeled "dN & dS for each branch") and also as branch lengths of your tree in section "dS tree:". ...
written 8 months ago by
al-ash • 60
0
votes
2
answers
6.0k
views
2
answers
Comment:
C: Unrooting Trees Help
... typo? `write.tree(unrooted_tr, "tree_unrooted.txt")` ...
written 8 months ago by
al-ash • 60
Latest awards to al-ash
Popular Question
10 days ago,
created a question with more than 1,000 views.
For Entrez Direct E-utilities - using match and xtract to filter by data value
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For "Optimal" setting of CPU and max_memory in Trinity
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How to append strings (from one file) to Fasta headers (in another file)
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Entrez Direct E-utilities - using match and xtract to filter by data value
Scholar
10 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Scholar
11 months ago,
created an answer that has been accepted.
For A: How to trim nucleotide sequences to length divisible by 3
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter
15 months ago,
voted at least 25 times.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1060 users visited in the last hour