distanceLow and insertLow parameter calculation

[sandrasan]

Hello,

I'm not sure what max{insert length - 1000, single read length} means for calculating distanceLow parameter. Can you elaborate?

Plus, I have several libraries with different insert sizes, how do I calculate it then?

Also, since I have several libraries, how do I calculate insertLow and High? --insertLow, let insert length be min{I1, I2}; for --insertHigh, let insert length be max{I1, I2} isn't much help since I have no idea what this means.

Thanks for your help.

[baoe]

See below.

---

From: sandrasan [[email protected]]
Sent: Tuesday, May 17, 2016 7:34 AM
To: baoe/AlignGraph
Subject: [baoe/AlignGraph] distanceLow and insertLow parameter calculation (#20)

Hello,

I'm not sure what max{insert length - 1000, single read length} means for calculating distanceLow parameter. Can you elaborate?

max{insert length - 1000, single read length} means: if insert length - 1000 is larger than single read length, then use insert length - 1000 as distanceLow; otherwise, use single read length as distanceLow.

Plus, I have several libraries with different insert sizes, how do I calculate it then?

Also, since I have several libraries, how do I calculate insertLow and High? --insertLow, let insert length be min{I1, I2}; for --insertHigh, let insert length be max{I1, I2} isn't much help since I have no idea what this means.

min{I1, I2} means: use the smaller insert length; max{I1, I2} means: use the larger insert length.

Thanks for your help.

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[sandrasan]

Thanks you for your help!

What would be my command with these parameters? I've put the one below and the only thing I get is a help message.

AlignGraph --read1 oat_R1.fasta --read2 oat_R2.fasta --contig oat-k41-scaf.fasta --genome oat_genomic.fasta --distanceLow 101 --distanceHigh 1068 --extendedContig oat-k41-extendedContigs.fa --remainingContig oat-k41-remainingContigs.fa --insertLow 68 --insertHigh 68

[GabrielaPinho]

Hi! I am having the same problems. I only get the help message with this command.

./AlignGraph --read1 Shotgun_1.fq --read2 Shotgun_2.fq --contig ABYSS60.fa --genome reference.fna --distanceLow 875 --distanceHigh 1125 --insertLow 294 --insertHigh 1000 --extendedContig Superscaffolds.fa --remainingContig Contigs_remaining.fa

When I remove "--insertLow" and "--insertHigh" from the command, the program runs for about 1 hour and show me the help message again. There are no error messages.

I really would appreciate some help here. Thank you

[baoe]

Hi,

Sorry for reply late. AlignGraph does not have an --insertLow or --insertHigh parameter.

Bao