Q&A about Anno-J Browser, jBuilder and simpleDB Tools:

1. Why did I get "Fatal error: Allowed memory size of 128M bytes exhausted (tried to allocate 32 bytes)"?

A. Your PHP program has 128M bytes available to it at runtime, all of which it has filled. The specific allocation which took the total memory usage from <128MB to >128MB was an allocation of 32 bytes. It took you over your memory limit. Please increase your memory_limit setting in the php.ini file.

2. While zooming out, some small exons in genes dispeared. It is annoying?!

A. The Anno-J browser uses Math.round() to calculate box width, that is Math.round(exon bases / resolutions). It would ignore small exons if their values were less than 0.5. Nevertheless, you could avoid it by setting boxWidthMin to 1 (default 0). As well as you should set option "-k keepSmall' to keep your small exons while formatting your data to simpleDB.

3. How can I display my methylation data outputted from methyl.py?

A. The simpleDB tool can format 8-column simpleText Meth data or 6-column methylation data with three classes CG, CHG and CHH into simpleDB folder. However, the results from methyl.py contain 7 columns and 16 classes. Therefore, it is necessary to convert them to simpleText or 6-column methylation data first, and then format it into simpleDB.

> cat allc_mpp1_*.tsv | awk '{if ($7==1) print $0}' | awk '{ if (substr($4,2,1)=="G") print $1"\t"$2"\t"$3"\tCG\t"$5"\t"$6; \
else if (substr($4,3,1)=="G") print $1"\t"$2"\t"$3"\tCHG\t"$5"\t"$6; else print $1"\t"$2"\t"$3"\tCHH\t"$5"\t"$6; }' > allc_mpp1.tsv

> php ~/simple_db_bin/simple_db.php -t SimpleMeth -i allc_mpp1.tsv -o mpp1

4. How can I configure a walkable track?

A. Since version 4.1.0 (aj-min8-src.js), AnnoJ browser can walk or jump from a locatin to another one within any type of tracks rather than the ModelsTrack only in 4.0.

1) create a file named 'walks.txt' with 4 columnes (uniq_id, chromosome, start, end) and put it into your simpleDB folder.
2) configure the track as 'showWalks : 1' in your configure file or checked in jBuilder tool.

5. Instead of having CHG for mammalian genome (makes no sense). I wonder if you can add CAC and CAG? We can click them on and off to immediately see the ES cell bias (CAG) vs. the brain bias (CAC).. but w need to then add mCH. so CG, CH, CAC and CAG?? would that be possible??? toggle on off?

A. It is implemented in version 4.1.1 (aj-min8-src.js).

1) use aj-min8-src.js (version 4.1.1).
2) type 'CG CAC CAG CH' text onto the 'Class' field while using the jBuilder Edit tool, or add a line of "class: 'CG CAC CAG CH';" to the MethTrack track in your AnnoJ.config object file.
3) format your data with these classes (CG CAC CAG CH) into simpleDB folder.

6. While I formated a lot sets of human reads into simpleDB, it caused inode usage problem. Is there any way to solve this problem?

A. This problem is caused by a lot of small cache files of reads. Yes. You can solve this by doing

1) increase computer inode configuration.
2) increase your cache size for reads, which means decrease your file number. You can change policies to -p "1:100:10" (bases 1: pixels 100: cache size increase 10 times). for example: php simple_db.php -t SimpleReads -i x.src -o y.out -p "1:100:10, 1:1". It uses only 10% inodes at 1:100 level.
3) add a line of new policy [policy : "1:100:10",] to your specific track in the annoj config file and use version 4.1.2 (aj-min8-src.js). Or add it [1:100:10] while using the jbuilder tool.