User: al-ash

gravatar for al-ash
al-ash60
Reputation:
60
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Japan/Okinawa/OIST
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10 hours ago
Joined:
3 years, 6 months ago
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Posts by al-ash

<prev • 59 results • page 1 of 6 • next >
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Answer: A: yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
... 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-ash60
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Answer: A: Manual edit of multiple alignment
... 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-ash60
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
... 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-ash60
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Comment: C: Platanus assembler : unable to start contig assembly, any problem with the comma
... 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-ash60
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Compare topologies of trees with non-identical tip labels
... 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 ...
R topology dendextend tanglegram tree written 5 months ago by al-ash60 • updated 4 months ago by jhc2.8k
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Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
... 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 ...
trimmomatic illumina adapter trimming pair-end written 6 months ago by al-ash60 • updated 5 months ago by finswimmer7.7k
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Comment: C: BLAST, setting maximum number of hits
... (typo: should be -max_target_seqs instead of -max_target_seqns) ...
written 8 months ago by al-ash60
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
... 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-ash60
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Answer: A: Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
... 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-ash60
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Comment: C: Unrooting Trees Help
... typo? `write.tree(unrooted_tr, "tree_unrooted.txt")` ...
written 8 months ago by al-ash60

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 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.

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