User: marongiu.luigi
marongiu.luigi • 60
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- United Kingdom
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- 1 year, 6 months ago
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Posts by marongiu.luigi
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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 4 weeks ago by
marongiu.luigi • 60
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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 4 weeks ago by
marongiu.luigi • 60
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Comment:
C: align fasta files using bowtie2
... however the resulting file is not a real alignment! ...
written 4 weeks ago by
marongiu.luigi • 60
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... 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 4 weeks ago by
marongiu.luigi • 60
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... 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 ...
written 4 weeks ago by
marongiu.luigi • 60
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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 7 months ago by
marongiu.luigi • 60
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... 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 ...
written 7 months ago by
marongiu.luigi • 60
• updated
7 weeks ago by
h.mon ♦ 6.6k
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... 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 7 months ago by
marongiu.luigi • 60
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... 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 ...
written 7 months ago by
marongiu.luigi • 60
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... 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 ...
written 7 months ago by
marongiu.luigi • 60
Latest awards to marongiu.luigi
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4 weeks ago,
created an answer that has been accepted.
For A: align fasta files using bowtie2
Popular Question
7 months ago,
created a question with more than 1,000 views.
For FastUniq on linux terminal
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