About required programs about ervcaller HOT 3 CLOSED

Hi Oh,

1. Yes in the latest version, I have replaced it by using Samtools. I have removed the corresponding comments in the README file.

2. I have uploaded it to the Database account.

3. It depends on your questions. There will be some redundancy in your database if you merge all of them. Especially for the HERVK sequences.

from ervcaller.

Hi Xun.

Thanks for reply.

I understood Q1, and Q2 due to your reply.

Then, I have remaining four questions about Q3.

1. I have four reference files from your program ; ERV_library.fa, HERVK.fa, Human_TE_library.fa, TE_consensus.fa

I want to detect and genotype "polymorphic endogenous retrovirus and other transposable element insertion" like your paper.

Thus, I want to find four types of polymorphic mobile elements in the human genome (All, LINE, SVA, ERV).

In this case, what is the best reference for me?

(Maybe, TE_consensus.fa or Human_TE_library or all of them?)

2. If you recommend to use two reference files (TE_consensus.fa, Human_TE_library), can I merge and use them following command lines?

$cat TE_consensus.fa Human_TE_library.fa > All.fa
$bwa index All.fa
$perl ERVcaller_v1.4.pl -i TE_seq -f .bam -H hg38.fa -T All.fa

3. TE_consense.fa is derived from human being?
   or a consensus of all species including human?

4. In your ERVcaller paper (10.1093/bioinformatics/btz205), did you use only TE_consensus.fa for TE reference?

Many thanks

Best,

Oh.

from ervcaller.

1. If you want to detect polymorphic ALU, LINE1, SVA, and ERV, like most tools, it is suggested to use the consensus FASTA sequences.
2. However, if you want, you can always merge references like what you listed.
3. Yes, it is derived from human beings.
4. I did run ERVcaller with various TE references instead of only using the TE_consensus.fa.

Best,
Xun

from ervcaller.