User: Seq225
Seq225 • 90
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Posts by Seq225
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... I have a set of 100 genes (the AA sequences) from a non-model plant species. Now I want to simply identify which pathways they belong to. I want to generate a typical KEGG style image/map highlighting my genes in the entire pathway.
I want to identify my genes that cluster in the same pathway.
Ho ...
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... I am working on horizontal gene transfer (HGT), and as part of my pipeline, making phylogenetic tree. I am using MAFFT for creating the alignment (MSA) and RAxML for tree building. As the analysis is to see if there is transfer of a gene from a distant clade, there are lot of ambiguities in the actu ...
written 4 months ago by
Seq225 • 90
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C: How to explain the blastx output?
... Thank you so much!!!!!!!!!!
It's now working!! ...
written 4 months ago by
Seq225 • 90
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C: How to explain the blastx output?
... Wow! Great. Thanks a ton. Almost there!!
I only know pieces about bash. So, confuse things.....
What I am using now is:
for i in seq_*
do
for j in *.dmnd
do
diamond blastp -p 30 --outfmt 6 --db $j --query $i -e 0.00001 -o ${i}_${j}.txt -k 5 --sensitiv ...
written 4 months ago by
Seq225 • 90
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Comment:
C: How to explain the blastx output?
... Thanks. I got the echo part.
I have been using diamond blastp (my db files are huge). However, I can now switch to regular blastp.
Thanks a ton for pointing out the e-value cut-off.
But, when I run the above loop, the output files are empty. ...
written 4 months ago by
Seq225 • 90
0
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Comment:
C: How to explain the blastx output?
... Thanks. I think I am putting the two variables "i", and "j" in a wrong way. I have added echo in my commands:
for i in seq_*
do
for j in *.dmnd
do
echo diamond blastp -p 30 -v --outfmt 6 --db echo "$j" --query echo "$i" -e 5 -o "$i".txt -k 5 --sen ...
written 4 months ago by
Seq225 • 90
0
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Comment:
C: How to explain the blastx output?
... Yes, it works!
However, my problem has an extra step. I have multiple queries (1067 to be exact). I want to run them in a loop. Like this:
**
for i in seq_*
do
for j in *.dmnd
do
diamond blastp -p 30 -v --outfmt 6 --db "$j" --query "$i" -e 5 -o "$i".txt ...
written 4 months ago by
Seq225 • 90
0
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1
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426
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Comment:
C: How to explain the blastx output?
... I have another question:
I want to run blastp against multiple db, and output 5 best hits (-max_target_seqs 5) from each of them (each db hits) . Suppose, I am running blastp against 5 db; I want all 25 hits into one output file.
I see that people use blastdb_aliastool. I just want your opinion. ...
written 4 months ago by
Seq225 • 90
1
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1
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426
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Comment:
C: How to explain the blastx output?
... Ya!!!!!
Thanks. Great that I can run command line to get all the sequences. I actually need to write a script with a loop to get sequences against my individual queries.
Thanks!! ...
written 4 months ago by
Seq225 • 90
0
votes
1
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426
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Comment:
C: How to explain the blastx output?
... Thank you very much!
I have used another program to get all the ORFs. Is have solved my concerns.
Now, I need something similar to qseq. Can I get the entire sequence of the subject? I want the fasta sequences of the top 5 hits for each of my queries. I do not see any options fro that on blast hel ...
written 4 months ago by
Seq225 • 90
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