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In looking at some of my datasets, I found that Tangram calls using BWA-MEM alignments passed through the TANGRAM_BAM tool ONLY show split-read calls. Not a single paired-end read was used for any MEI…
RPSeq updated
9 years ago
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Hi,
In your paper, you say that you "discard those reads with low alignment quality, including MAPQ < 20, aligned length < 30 nt and FLAG with UNMAP, SECONDARY, QCFAIL (and DUP if UMI is not applic…
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Hello!
I was wondering if `methylpy` methylation calling takes care of directional and non-directional libraries? To quote Bismark User guide here
> Bisulfite treatment of DNA and subsequent PCR…
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### INIT:
1. local gets paratext project, tokenizes, creates TokenizedCorpus
2. Creates relationships, parallelizes, creates alignments.
3. Project pushed to server TIMESTAMP1.
4. `server.PutPro…
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I'd like to filter out alignments with an alignment score (`AS:i`) less than some threshold.
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## What problem does this address?
Some alignment tools, e.g. Justification, are present in both the block toolbar and the Inspector.
Others, e.g. Vertical Alignment, Alignment (normal width, wid…
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Hi
I've been running Cactus on 3 different Barley genomes (planning to scale up to more genomes later). I've been running each job to create alignments of each chromosome from 1 to 7. I'm breaking …
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```
The reason for this is limited by the size of exact hit, which was 199 in
version of 0.2.9.4 or before. In 0.2.9.4, you can enlarge the number of matches
by using -k 1000, which allow 1000 align…
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As discussed here: https://github.com/rednex/rgbds/issues/133
This could either be done in source code or by using the linkerscript.
```
SECTION "Code", ROMX
...
SECTION "Data", ROMX, BANK["Cod…
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Greetings,
I've noticed that alignments break over small deletions. Is there a way to control the size of deletion an alignment can contain?
Thank you,
Zev
zeeev updated
7 years ago