Comments (5)
Hi @whiteorchid I have a problem with running ERV, could you help me to check this issue?
#7
Best,
Jian-Guo
from ervmap.
Thanks for your message!
I used ERVmap by installing it in the traditional way, not by the Docker method. Maybe you can check if the bed files and the ref genome version are matched.
Best,
from ervmap.
Hi @whiteorchid Thanks for your message. Could you please share your install code with me?
I just used conda, but some package is not available...
Best,
from ervmap.
Sorry, currently I do not have access to the previous server.
I find the trim script kindly given by Professor Kong. For all other processes, I just follow the instructions on the Github page.
#!/usr/bin/perl -w
#
# a simple program for post-processing paired-end reads after btrim trimming
#
# Yong Kong
# Yale University
#
use strict;
my $f1 = shift; # summary file 1
my $f2 = shift; # summary file 2
my $s1 = shift; # trim output file 1
my $s2 = shift; # trim output file 2
my $check = shift || 0;
die "usage: $0 <summary file 1> <summary file 2> <trim output file 1> <trim output file 2>" unless ($f1 && $f2 && $s1 && $s2);
my ($fh1, $fh2);
my ($sh1, $sh2);
my ($oh1, $oh2);
my ($ph1, $ph2);
open($fh1, "<$f1") || die "cannot open $f1";
open($fh2, "<$f2") || die "cannot open $f2";
open($sh1, "<$s1") || die "cannot open $s1";
open($sh2, "<$s2") || die "cannot open $s2";
my $o1 = "${s1}.pe"; # reads in both ends passed
my $o2 = "${s2}.pe";
my $p1 = "${s1}.se"; # read in trim file1 passed, but the pair in file2 failed
my $p2 = "${s2}.se"; # read in trim file2 passed, but the pair in file1 failed
open($oh1, ">$o1") || die "cannot open $o1";
open($oh2, ">$o2") || die "cannot open $o2";
open($ph1, ">$p1") || die "cannot open $p1";
open($ph2, ">$p2") || die "cannot open $p2";
while (my $l1 = <$fh1>, my $l2 = <$fh2>) {
chomp($l1);
my @t1 = split(/\t/, $l1);
my $n1 = $t1[0];
my $s1 = $t1[1];
chomp($l2);
my @t2 = split(/\t/, $l2);
my $n2 = $t2[0];
my $s2 = $t2[1];
if ($check) {
my ($n11, $n12);
my ($n21, $n22);
my $dummy;
($n11, $dummy, $n12) = ($n1 =~ /(.*)(\s+|\/)(1|2)/);
($n21, $dummy, $n22) = ($n2 =~ /(.*)(\s+|\/)(1|2)/);
die ">$n11< ne >$n21<" if ($n11 ne $n21);
die ">$n12< == 1" unless ($n12 == 1);
die ">$n22< == 2" unless ($n22 == 2);
}
if ($s1 eq 'Pass' && $s2 eq 'Pass') {
&find_and_print($sh1, $oh1, $n1);
&find_and_print($sh2, $oh2, $n2);
} elsif ($s1 eq 'Pass') {
&find_and_print($sh1, $ph1, $n1);
} elsif ($s2 eq 'Pass') {
&find_and_print($sh2, $ph2, $n2);
}
}
close($fh1);
close($fh2);
close($sh1);
close($sh2);
close($oh1);
close($oh2);
close($ph1);
close($ph2);
print "Done!\n";
sub find_and_print {
my ($ih, $oh, $name) = @_;
while (defined(my $sl = <$ih>)) {
chomp($sl);
my @t = split(/\t/, $sl);
my $n = $t[0];
if (substr($n, 1) eq $name) {
print $oh "$sl\n";
$sl = <$ih>;
print $oh "$sl";
$sl = <$ih>;
print $oh "$sl";
$sl = <$ih>;
print $oh "$sl";
last;
}
}
}
from ervmap.
Hey @whiteorchid thanks for your reply.
This is my code.
dir=~/PRJNA82747
index=~/t12a/reference/hg38_ek12/STAR_index_star_2.7.6a
erv_bed=/home/zhou/soft/ERVmap
mkdir -p ERV.map
cd ${dir}/ERV.map
mkdir -p results
cd ${dir}/ERV.map/results
singularity exec \
--bind ${dir}/raw:/data:ro \
--bind ${index}:/genome:ro \
--bind ${erv_bed}:/resources:ro \
--bind ${dir}/ERV.map/results/${i}:/results \
~/singularity/ervmap.1.2.1.sif /scripts/ERVmapping.sh \
--read1 ${dir}/raw/${i}_1.fastq.gz --read2 ${dir}/raw/${i}_2.fastq.gz \
--output ${i} -m ALL \
--cpus 12 --limit-ram 151290751290 -d
I just used GRCh38.primary_assembly.genome.fa and gencode.v34.annotation.gtf for STAR_index_star_2.7.6a.
Best,
Jian-Guo
from ervmap.
Related Issues (11)
- installation / usage instructions HOT 17
- How was ERVmap.bed generated? HOT 1
- out of order record
- Failed to run the jobs
- ERVresults.txt didn't detect any ERVmap HOT 13
- btrim - the requested version (0.3.0) is not available any more HOT 6
- /usr/bin/python2.7 htseq.script.count not found HOT 1
- Differential analysis HOT 2
- ERV normalisation questions
- Question about ERV family in ERVmap.bed file
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from ervmap.