Swish Tools Download

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I see it on TV all the time, good looking swish pans. I'm assuming it's the BCC swish pan. I get do it nicely in FCP with the push blur transition. I'm not sure how to do it properly with BCC. It seems to start abruptly and not really ease in and out. Does anyone here have experience on producing a nice swish pan with BCC? Thanks.

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Well, for some odd reason, I can't get a screen grab off my system this morning, but here's what I do. I've found the best "look" for the ballistics of this effect is when the transition duration is between 10 and 15 frames. In that case, I'll pretty much stick to the default levels. If a longer transition is used, say 1 to 2 seconds, I'll add a third keyframe in the middle of the transition, increase the blur amount about 10 to 15 % and adjust scaling for about a 50% zoom in. And you are correct in that regardless of the overall direction chosen for the swish, the blur is added in both directions rather than one. There does not seem to be an option to change that, or at least not that I've been able to find, to control the direction of the blur itself.

For a swish pan take two pieces of media, cut them back to back, and use a push effect of about 6 frames centered on the cut. On the video track above it add edit points about 6 frames before and after the cut. Apply a blur effect, horitzontal only, and keyframe it from 0 to a pretty decent blur at the cut, then back down to 0. Apply a color effect to the filler, keyframe the luma range whites from 235 to 0 at the cut, then back to 235 at the end of the filler. This will blur the footage right before the push, then blur the push so you don't notice it's two pieces of media back to back, and blow out the whites.

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I've been recently learning about pseudoalignment tools for transcript quantification like kallisto and salmon. However, I couldn't find anywhere information about their usefulness for non-annotated isoforms and aberrant splicing events.

Apologies for this sort of nonanswer but the tl;dr is that your analysis is more complicated than one might think. If anything, I'd try out a couple of different tools and a few different options for each tool and check the agreement, and also using different tools for different purposes is not a bad idea either.

I suppose we should call these unique fragment identifiers (UFIs) instead of UMIs. Nonetheless, I think the UMI counting procedure used by kallisto and other tools should work just fine, but keeping in mind that longer genes will get more counts because they generate more fragments (at least amplification bias will be removed though).

Keep me posted on this, but kallisto can definitely handle this type of data (bustools can do the UMI collapsing and kallisto can leverage the final UMI count matrix to do its traditional quantification with effective length normalization) and this data would be super interesting to look at.

My input samples come split into 1-5 lanes/libraries/fastq files. Each of these blobs comes in 3 fastq.gz files: R1 (first read of pair), R2(UMI), R3 (second read of pair). I used zcat + umitools to collapse all the libraries of my samples into a single "fastq" per sample, and using UMItools to add the UMI to the read header. This way I end up having only a pair of R1 / R2 fastq.gz files per sample.

First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way" of handling UMIs). I'm a bit busy with other developments to kallisto right now, but I might consider adding UMI-tools interfacing with kallisto, especially if it's a desired feature. For now, if you really want to use UMI-tools, you should take those read header sequences and put them back into a separate FASTQ file. If you have 3 FASTQ files, that's fine -- kallisto can handle that.

If it ends up working and you want to describe the methods in the manuscript, just write out the code above and say: "we used kb_python commit number: 73c62d77e894a39f2fd99370878ce895984186b8, and kallisto (version 0.49.0) commit 51a22e92e9c81203c53a596a8e3f95ae85e77865 and bustools (version 0.42.0)" so others can reproduce the results.

I can try introducing a new commit into kallisto that recapitulates the abundance.tsv structure from the mtx files sometime this week or next week to make it more usable with tools like tximport/swish/sleuth/etc..

The pipelines have been written to work together seamlessly and should satisfy the 75% of your goals that start with "Differentially Expressed". For splicing analysis, there is another pipeline in the making called rnasplice, but it has no stable releases yet, and I do know nothing about its development status. However, feel free to join the nf-core Slack and ask the developers directly in the respective channel. You can surely get some inspiration regarding useable tools and parameters there.

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I was also disappointed by the lack of support for importing Adobe Illustrator or Macromedia Freehand files. Many designers use these as their primary tools for building graphics. I found it annoying to have to export my Illustrator graphics as WMF files and then import them into SWiSH.

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interaction:The interaction tests are different than theother tests produced by swish, in that they focus on a differencein the log2 fold change across levels of x when comparingthe two levels in cov. If pair is specified, thiswill perform a Wilcoxon rank sum test on the two groupsof matched sample LFCs. If pair is not included, multiplerandom pairs of samples within the two groups are chosen,and again a Wilcoxon rank sum test compared the LFCs across groups.

I'm looking for any open source command line tool or tools which will allow me to index and search a large number of plain text files. Approximate search would be a plus. The tool only needs to print the files that match, although some match context would be useful. A GUI tool isn't useful for my application, nor is anything that searches files one by one (grep for example). I'm basically targeting unix platforms (osx, linux, bsd).

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