User: Seq225

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Seq22590
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Posts by Seq225

<prev • 68 results • page 1 of 7 • next >
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How to do simple pathway analysis?
... 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 ...
genome gene rna-seq written 5 weeks ago by Seq22590 • updated 5 weeks ago by SMK1.4k
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Should I remove GAPs from alignment before making phylogenetic tree?
... 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 ...
genome gene next-gen rna-seq alignment written 4 months ago by Seq22590
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Comment: C: How to explain the blastx output?
... Thank you so much!!!!!!!!!! It's now working!! ...
written 4 months ago by Seq22590
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Comment: 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 Seq22590
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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 Seq22590
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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 "$i".txt -k 5 --sen ...
written 4 months ago by Seq22590
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Comment: C: How to explain the blastx output?
... Yes, it works! However, my problem has an extra step. I have multiple queries (1067 to be exact). I want to run them in a loop. Like this: ** for i in seq_* do for j in *.dmnd do diamond blastp -p 30 -v --outfmt 6 --db "$j" --query "$i" -e 5 -o "$i".txt ...
written 4 months ago by Seq22590
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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 Seq22590
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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 Seq22590
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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 Seq22590

Latest awards to Seq225

Popular Question 4 months ago, created a question with more than 1,000 views. For Bismark Methyl-Seq Analysis
Supporter 4 months ago, voted at least 25 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For Bismark Methyl-Seq Analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For HOMER annotatePeaks.pl problem
Popular Question 20 months ago, created a question with more than 1,000 views. For De Novo Assembly of small RNA Reads (Illumina)

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