User: marongiu.luigi

Reputation:
60
Status:
New User
Location:
United Kingdom
Last seen:
2 months, 4 weeks ago
Joined:
1 year, 8 months ago
Email:
m*************@gmail.com

Posts by marongiu.luigi

<prev • 42 results • page 1 of 5 • next >
0
votes
1
answer
284
views
1
answers
Comment: C: align fasta files using bowtie2
... thank you! this was a fast alternative to bowtie. the problem is how to convert the sam file to an aligned fasta. I ran: bbmap.sh in=your.fa out=align.sam ref=ref.fa samtools view -Sb align.sam > align.bam samtools sort align.bam align_srt samtools index align_srt.bam sa ...
written 12 weeks ago by marongiu.luigi60
0
votes
1
answer
284
views
1
answers
Comment: C: align fasta files using bowtie2
... thank you! it is possible to convert the file back into fasta directly? I tried with samtools bam2fq 16S_africanum_srt.bam.bai | seqtk seq -A > 16S_africanum.fa but i got: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header ( ...
written 12 weeks ago by marongiu.luigi60
0
votes
1
answer
284
views
1
answers
Comment: C: align fasta files using bowtie2
... however the resulting file is not a real alignment! ...
written 3 months ago by marongiu.luigi60
0
votes
1
answer
284
views
1
answers
Answer: A: align fasta files using bowtie2
... Sorry, that was a silly question. the problem was in the input file: the option -q stands for fastq files; -f is for fasta and multifasta. Using bowtie2 -f -x ref_idx -U input.fa -S output_aln resulted in the alignment. Case closed. ...
written 3 months ago by marongiu.luigi60
1
vote
1
answer
284
views
1
answer
align fasta files using bowtie2
... dear all, it is possible to use bowtie2 to align fasta files rather than fastq? essentially I would like to use bowtie just like an aligner such as muscle, taking advantage of the greater computational speed of the former. In the handbooks I found that this is possible but there is no example. I c ...
genome alignment sequencing written 3 months ago by marongiu.luigi60
0
votes
1
answer
368
views
1
answers
Comment: C: Mauve on Ubuntu 16
... PS: launching the GUI version I got the error: "the sequences might not have any homologous regions" which silly since the sequences are from variants of the same species ...
written 9 months ago by marongiu.luigi60
0
votes
1
answer
368
views
1
answer
Mauve on Ubuntu 16
... Dear all, I installed Mauve with the following: apt-get install mauve-aligner and then I ran it with the following: mauveAligner --output=ery.mauve --output-alignment=ery.alignment ery_multiseq.fasta where ery_multiseq.fasta is the fasta file with the different sequences I want to align ...
software error alignment written 9 months ago by marongiu.luigi60 • updated 3 months ago by h.mon8.0k
0
votes
0
answers
340
views
0
answers
Comment: C: Install MAFFT on Ubuntu 16 non standard folder
... I wanted to try version 7.222 because I had problems of memory availability with muscle; maybe mafft is better especially is ver. 7.222 is less RAM demanding... ...
written 9 months ago by marongiu.luigi60
0
votes
0
answers
340
views
0
answers
Install MAFFT on Ubuntu 16 non standard folder
... Hello, I am trying to install MAFFT on my Ubuntu Xenia machine. I downloaded the tar archive 'mafft-7.222-with-extensions-src.tgz', extracted and called the folder 'mafft'. I moved the folder to '/usr/local/lib/' and tried to follow the instructions for the [installation on non standard location][1 ...
software error alignment written 9 months ago by marongiu.luigi60
0
votes
0
answers
341
views
0
answers
muscle 'Non-zero return code 137' or 'Killed43' status
... Dear all, I would like to use biopython to align some DNA sequences. I got a script from internet and I ran it as follows (~ is the short for my home path): ~$ python Python 3.5.1 (default, Jul 3 2016, 12:57:35) [GCC 5.4.0 20160609] on linux Type "help", "copyright", "credits" or ...
software error alignment written 9 months ago by marongiu.luigi60

Latest awards to marongiu.luigi

Scholar 3 months ago, created an answer that has been accepted. For A: align fasta files using bowtie2
Popular Question 9 months ago, created a question with more than 1,000 views. For FastUniq on linux terminal

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 488 users visited in the last hour