can use WBA for step2

[zyworship]

Hi,
I want to ask for some help about the step 2;
Step 1. java -jar PotentialMEIReadFinder.jar
Step 2. Now do the mobiome mapping on the resulting .fq file with MOSAIK
Step 3. java -jar RefAndMEPairFinder.jar
Step 4. java -jar AnchorClusterer.jar

could I use bwa for mapping in step2?

[jyhehir]

Hi, When we originally developed mobster, we had better results with mosaik in comparison to bwa. But of course bwa has also evolved in the mean time.The theoretical answer is, yes. But I personally haven't tried it. But happy to hear how it goes. On Thursday, 4 July 2019, 11:27:44 am GMT+2, zyworship <[email protected]> wrote: Hi, I want to ask for some help about the step 2; Step 1. java -jar PotentialMEIReadFinder.jar Step 2. Now do the mobiome mapping on the resulting .fq file with MOSAIK Step 3. java -jar RefAndMEPairFinder.jar Step 4. java -jar AnchorClusterer.jar could I use bwa for mapping in step2? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[zyworship]

Hi,
thanks for your reply.
I have download the version :0.2.4.1. I have change the code "MOBIOME_MAPPING_CMD=bwa mem -o (OUT_FILE).bam /GS01/project/chejing_group/chej5t1/software/mobster-master/resources/mobiome (FASTQ)" in the Mobster.properties file.
I want to test the bwa, but it come out the error like this:
mem: invalid option -- 'o'
Exit value: 1
44879 [main] FATAL Mobster - Mobiome mapping finished with non-normal exit value: 1
44879 [main] FATAL Mobster - Therefore Mobster execution is terminated
I don't know where is the problem.

Another question;
How to make the file "54_mobiles_inclHERVK.dat"; I don't find the statement for this file.
Thank you so much

[SHuang-Broad]

@zyworship

1. you command pointed bwa mem to a directory holding references that (I believe) specifically designed for MOSAIK, so it won't work
2. 54_mobiles_inclHERVK.dat is from MOSAIK, which doesn't seem to be maintained anymore. You need to have your own MEI-purposed reference (FASTA format) for bwa mem. These references are available (possibly not exclusively) from RepBase, but it is not free, from what I understand.
3. Once you have the correct MEI reference, bwa mem should work, as I have successfully run that (sorry, I cannot share the reference per license agreement).