eiigt.over-blog.com/
18 Janvier 2021
GSnap is an auto-tune effect. It can be used subtly to correct the pitch of a vocal, or, with more extreme settings, to create a robot-voice effect. It requires a monophonic input signal to operate.
GSnap is a very simple-to-use software application that can capture the screen and automatically save image files on the computer. It doesn't include complex options or customization preferences, making it accessible to all types of users.
Before proceeding any further, you should know that the app hasn't been updated for a long time, and some of its features are no longer functional. For instance, it integrates a feature for automatically uploading screenshots to the developer's website and provides you with the direct link in the Clipboard. However, the host is no longer working, so the URL returns an error.
This is a portable package, so it doesn't require installation. It means that you can save the program files anywhere on the hard drive or on a removable storage unit, and just click the executable to launch GSnap. Just make sure the external device is not write-protected, since the tool needs to create image files in the same location as itself.
Although it doesn't show a balloon message to attract your attention, the app creates an icon in the systray area at startup, thus providing quick access to capturing the screen.
It lets you draw the exact region you want to capture and showing the region's height and width (in pixels), along with the RGB color code of the current cursor position. Plus, you can fine-tune the region using the arrows as well as the Shift key in combination with the arrow keys to change its position by 1 or 10 pixels.
The current area is also magnified in a small frame. Once the capture is accepted, GSnap automatically saves it as a JPEG file and placed it the same location as the program.
The app worked well in our tests, without triggering the OS to hang, crash or prompt error messages. Unsurprisingly, it had minimal impact on computer performance, using low CPU and RAM. However, not all of GSnap's features are functional. Otherwise, it proves to be a pretty basic screenshot grabber for rookies.
top alternatives FREE
top alternatives PAID
GMAP is a tools for rapidly and accurately mapping and aligning cDNAsequences to genomic sequences.
GSNAP is designed to align short reads from NGS data and allow detection ofshort and long range splicing de novo or with a database of know juctions. Inaddtion, SNP-tolerant alignements and alignments of reads obtained frombisulfite treated DNA are implemented.
There may be multiple versions of gmap-gsnap available. An easy way of selecting theversion is to use modules. To see the modulesavailable, type
To select a module use
where [version] is the version of choice.
gmap-gsnap is a multithreaded application. Make sure to match thenumber of cpus requested with the number of threads.
Starting with release 2014-04-01 gmap/gsnap switched to a new index format.Indices are stored under
/fdb/gmap_post20140401/[organism]/[source]/[build]/Sequence/gmap-gsnap
[organism] is the specific organism of interest (Gallus_gallus, Rattus_norvegicus, etc.)[source] is the source for the sequence (NCBI, Ensembl, UCSC)[build] is the specific genome build of interest (hg19, build37.2, GRCh37)in a structure analogous to the igenomes package. In addition, commonly usedgenomes are also available at/fdb/gmap_post20140401/common_genomes. This path is also thedefault path gmap and gsnap use to look for genome files, so a particular genomeis available there it is sufficient to provide the genome name with -dgenome_name to any of the tools without also specifying the genomedirectory with -D.
Gsnap throughput was measured using different numbers of threads with anENCODE data set (100nt single ended RNA-Seq, mouse Purkinje cells; accession ENCFF220BOE; biosample ENCSR758TAD). Discovery of novel splice sites was disabled but knownsplice sites were provided as input. The input file was compressed and storedon local scratch space. The output was saved unmodified on local scratch space. Eachprocess was allocated 30GB of memory. The exact command used was
Reads aligned per second per thread for different versions of gsnap with different numbers of threads.
The lower throughput of version 2015-05-01 with default settings is largely the result of a change in the default for one setting ( --end-detail) from medium to high which has the effect of improving alignments in the small number of cases where the distal end of a splice or indel contains a mismatch. Changing this version back to medium recovers most the loss in throughput. It is therefore largely a tradeoff between throughput and sensitivity. As of version 2016-06-30, the default reverted to medium.
Most benchmarks were run on the phase1 norm nodes (x2650; 10g). Benchmarks ending in x2695 were run on the newer phase2 norm nodes (x2695; ibfdr). Google drive for mac os x yosemite.
Gsnap scales well with the number of threads all the way to 32, though the mostefficient use is probably around 24 threads with this input data set. Note that gsnap does not start any extra processes or threads, so --nthreads=$SLURM_CPUS_PER_TASK is appropriate unless the output ispiped into another process such as samtools. In that case the number of threads usedby the second process has to be subtracted from the number of threads given togsnap.
Performance was comparable when input and output were kept on the shared storagespace (/data).
Gmap and gsnap are multi-threaded applications. The thread count isdetermined with -t / --nthreads and defaults to 1. Please do notrun with more than 2 threads on the interactive helix system.
Map and align a single cDNA to the mouse genome. Note that the mouse genomeis in common genomes, so no path has to be provided.
Map and align single end RNA-Seq data from encode to the mouse genome withdatabase of known splice junctions. Supress search for novel juctions:
A number of other small tools are available as part of the package.
Batch scripts should use the $SLURM_CPUS_PER_TASK environmentvariable to determine the number of threads to use. This variable is set byslurm according to the number of requested cores. An example script for gsnapmight look like the following:
The script is submitted to the batch system requesting, for example, 8 coresand 25GB of memory:
Set up a command file for two jobs, each aligning single ended reads. Notethat swarm allows line continuations.
Create the known splice site database as shown above and start the jobs with swarm
Interactive work requiring significant resources should be carried out oninteractive compute nodes, not on the head node or helix. Interactive nodes areallocated with sinteractive. For example, to request a 8 coreinteractive job with 25GB memory:
On the interactive node, gmap and gsnap are then used essentially as decribedabove.
/image%2F6176875%2F20210220%2Fob_309245_converting-formulas-to-values-using-ex.jpeg)
/image%2F6176875%2F20210220%2Fob_0f66df_movavi-chiliburner-3-activation-key.jpeg)
/image%2F6176875%2F20210220%2Fob_dcf9d4_igo-primo-gps-software-windows-ce-5-so.jpeg)
/image%2F6176875%2F20210220%2Fob_e67afe_honda-cb-600-hornet-2008-owners-manual.jpeg)