Uame-Purple-merge - para listas de fatores de transcricao x qantidade de transcritos

cat Uame-Purple-merged.list.txt | cut -f 2,3 | sed 's,|,\t,g' | cut -f 2,4 | nsort -u | cut -f1 | nsort | uniq -c

Comentários

Postar um comentário

Postagens mais visitadas deste blog

Instalar o VMPlayer no Linux Ubuntu

Quando fui instalar o VMPlayer no Linux encontrei o seguinte erro: Extracting VMware Installer...done. Installing VMware Player Application 15.5.0 Copying files... Configuring... bora/lib/string/str.c:284 Buffer too small VMware Workstation Error: VMware Workstation unrecoverable error: (host-9802) bora/lib/string/str.c:284 Buffer too small You can request support.  To collect data to submit to VMware support, choose "Collect Support Data" from the Help menu. You can also run the "vm-support" script in the Workstation folder directly. We will respond on the basis of your support entitlement. A solução foi: sudo LC_ALL=C ./VMware-Player-15.5.0-14665864.x86_64.bundle
Leia mais
 Retirado de: https://playingwithgenomics.wordpress.com/2015/07/15/producing-a-bam-file-and-extracting-unique-reads-from-bowtie2-results/ I am always looking for ways to keep my disk usage down. Especially since I’ve been mapping close to 100 Chip-Seq files. I find that 1) piping Bowtie2 output into samtools to create a bam file and 2) keeping only the uniquely mapped reads help a lot. Here is how I do those: I’m dealing with single-end data here. You can modify the command if you are dealing with paired-end data. Text written in red should be substituted according to your data. Converting Bowtie2 output to bam file bowtie2 -x BOWTIE2_INDEX -\ -p NUM_THREADS \ -U INPUT_FILE.fastq.gz | samtools view -bS -t \ YOUR_GENOME_INDEX.fa.fai - > output.bam Counting unique reads You basically can exploit the XS tag that are set by Bowtie2  for reads that can be mapped in multiple places. Therefore, uniquely mapped reads lack the XS tag. The following command exclude u...
Leia mais