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Results tagged with phylogenetics
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user 6251
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
5
votes
Cannot obtain alignment summary after running Bowtie2
Remove the --quiet option, and capture STDERR as well as STDOUT:
bowtie2 -x human_mirs -U 1.lane.clean.gz -N 1 --norc --no-unal --no-head --ignore-quals 1>sr1prueba.sam 2>sr1prueba.summary.log
See al …
- 841
3
votes
Error with BWA Mem input having multiple fastq files using cat and process substitution
AS both the OP and @MaximilianPress suggested, the paired-end reads should be provided as 2 separate arguments to bwa. This is true whether the reads are in files or streamed. For the sake of complete …
- 841
4
votes
Accepted
Edit all the fasta headers using awk
EDIT after OP's update:
Try this Perl one-liner:
perl -pe 'BEGIN { $i = 1 } $i += s{>([^_]+)_.*_}{>RNA${i}#${1}/}' input_file > output_file
Here, the command line flags are:
-e: tells the perl int …
- 841