Illegal division by zero about ervcaller HOT 8 CLOSED

It is not allow to have insert size = 0, i will further specify it in the updated manual.

Meanwhile, the term of "insert size" we used here included the read length, thus it won't be 0 even you the two paired-end have overlapped sequences. For example, the 100 bp paired-end reads have 30 bp overlapped regions, the insert size should be 170 bp (100+100-30)

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Thanks! What option I should use? --l (length_insertsize) or -L (L_std_insertsize)

from ervcaller.

Ideally you should use both, -l is the mean value and -L is the std. You can calculate it using many other tools, such as GATK.

If you don't use both of them, ERVcaller can calculate it using implemented tool. let me know if the implemented tool cannot accurately calculate it.

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I have a fasta file that contain 90 TE sequence，do you mean that I should calculating the average TE length and standard deviation of TE length before running ERcaller？

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The insert size is a used for the NGS data not the 90 TE reference sequences in FASTA format.

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Sorry, I don't understand. : )

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you can check this page about insert size: http://software.broadinstitute.org/software/igv/interpreting_insert_size. You can find more with the key words such as "NGS insert size"

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Thanks!

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