User: Audrey
Audrey • 20
- Reputation:
- 20
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- New User
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- France
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- 20 hours ago
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- 1 month, 2 weeks ago
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Posts by Audrey
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... Thank you for your answer.
The solution you mentioned is still valid but doesn't solve my main issue here. How can I add to the cart thousand of genes using their IMG IDs?
Or is there any other way such as fastq-dump for the NCBI database? ...
written 2 days ago by
Audrey • 20
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... Hi all,
I tried to look online before asking here but couldn't find any reliable solutions.
I have thousands of IMG gene IDs in a simple .txt file. I would like to download the **protein** sequences associated.
Is there an automatic way to do that?
Thank you for your help! ...
written 2 days ago by
Audrey • 20
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... Hi all,
I have paired-end reads for a genome and a specific contig of interest. I would like to prolong my contig as much as possible using PRICE.
I tried the following command line:
./PriceTI -fp L_raff_FAM23217_raw_reads_1.fq L_raff_FAM23217_raw_reads_2.fq 150 -icf contig.fasta 1 1 5 -o con ...
written 6 days ago by
Audrey • 20
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... Thank you for your help Joe. I also tried what you suggested and studied the gene content within my contig of interest. Despite the genes of interest (that could have both origin), no other genes are located on this contig.
I'm kind of stuck now with this problem.. Anyway, thanks again! ...
written 9 days ago by
Audrey • 20
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... Hi all,
I have paired-end reads of a lactococcal strain and its assembly.
I want to determine the origin of a specific contig of interest to known if its from a plasmid or a chromosomal origin.
I tried mapping the reads using bbmap, extension of contigs to study the termini, etc. but so far I h ...
written 9 days ago by
Audrey • 20
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... Thank you so much shelkmike! ...
written 9 days ago by
Audrey • 20
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... Thank you for your suggestion genomax! ...
written 12 days ago by
Audrey • 20
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5 follow
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... Hi all,
I have raw sequencing datas of metagenomes and all of them are single-end reads.
I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG., *et al*, 2013) but it only works with paired-end reads ...
Do you have any recommendation on what software could I use?
Thank you for yo ...
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... Thank you cpad0112 for your help! Both commands work great. Even if I understand better the `rename` command than the `parallel` one.
That's so useful, thanks again! ...
written 5 weeks ago by
Audrey • 20
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... Thank you so much RamRS for your help!
I run the following script and it worked great:
#!/bin/bash
for file in * ;
do
mv ${file} $(echo $file | sed 's/.fasta.*/.fasta/');
done
Thank you again, have a nice day. ...
written 5 weeks ago by
Audrey • 20
Latest awards to Audrey
Supporter
6 weeks ago,
voted at least 25 times.
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to keep the top hits only in the output file of hmmscan?
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