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  • cmccabe
    replied
    bedToBam

    dnascopev@ubuntu:~/samtools-0.1.19$ make
    make[1]: Entering directory `/home/dnascopev/samtools-0.1.19'
    make[2]: Entering directory `/home/dnascopev/samtools-0.1.19'
    make[2]: Nothing to be done for `lib'.
    make[2]: Leaving directory `/home/dnascopev/samtools-0.1.19'
    make[2]: Entering directory `/home/dnascopev/samtools-0.1.19/bcftools'
    make[2]: Nothing to be done for `lib'.
    make[2]: Leaving directory `/home/dnascopev/samtools-0.1.19/bcftools'
    make[2]: Entering directory `/home/dnascopev/samtools-0.1.19/misc'
    make[2]: Nothing to be done for `lib'.
    make[2]: Leaving directory `/home/dnascopev/samtools-0.1.19/misc'
    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
    bam_tview_curses.c:5:20: fatal error: curses.h: No such file or directory
    compilation terminated.
    make[1]: *** [bam_tview_curses.o] Error 1
    make[1]: Leaving directory `/home/dnascopev/samtools-0.1.19'
    make: *** [all-recur] Error 1

    seems that a GNU ncurses library didnt install:
    I tried-
    $ wget http://ftp.gnu.org/pub/gnu/ncurses/ncurses-5.7.tar.gz
    $ tar xzf ncurses-5.7.tar.gz
    $ cd ncurses-5.7
    $ ./configure --prefix=/opt/ncurses
    $ make
    # make install
    $ ls -la /opt/ncurses

    and got no opt/ncurses
    dnascopev@ubuntu:~/ncurses-5.7$ ls -lt
    total 1621
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:22 c++
    drwxrwxr-x 2 dnascopev dnascopev 1024 Jul 13 08:22 lib
    drwxrwxr-x 2 dnascopev dnascopev 9216 Jul 13 08:22 objects
    drwxr-xr-x 3 dnascopev dnascopev 1024 Jul 13 08:22 misc
    drwxr-xr-x 2 dnascopev dnascopev 5120 Jul 13 08:22 test
    drwxrwxr-x 2 dnascopev dnascopev 9216 Jul 13 08:21 obj_g
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:21 include
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:20 progs
    drwxr-xr-x 7 dnascopev dnascopev 1024 Jul 13 08:20 ncurses
    drwxr-xr-x 2 dnascopev dnascopev 5120 Jul 13 08:20 man
    -rw-rw-r-- 1 dnascopev dnascopev 61167 Jul 13 08:20 config.log
    -rwxrwxr-x 1 dnascopev dnascopev 40288 Jul 13 08:20 config.status
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:20 form
    -rwxr-xr-x 1 dnascopev dnascopev 901 Jul 13 08:20 headers.sh
    -rw-rw-r-- 1 dnascopev dnascopev 5723 Jul 13 08:20 Makefile
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:20 menu
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 13 08:20 panel
    -rw-rw-r-- 1 dnascopev dnascopev 19692 Jul 13 08:20 edit_man.sed
    -rwxr-xr-x 1 dnascopev dnascopev 4286 Jul 13 08:20 edit_man.sh
    drwxr-xr-x 5 dnascopev dnascopev 1024 Nov 2 2008 Ada95
    drwxr-xr-x 3 dnascopev dnascopev 1024 Nov 2 2008 doc
    -r--r--r-- 1 dnascopev dnascopev 71037 Nov 2 2008 INSTALL
    -r--r--r-- 1 dnascopev dnascopev 22626 Nov 1 2008 ANNOUNCE
    -r--r--r-- 1 dnascopev dnascopev 23685 Nov 1 2008 announce.html.in
    -r--r--r-- 1 dnascopev dnascopev 7195 Nov 1 2008 dist.mk
    -r--r--r-- 1 dnascopev dnascopev 416617 Nov 1 2008 NEWS
    -r-xr-xr-x 1 dnascopev dnascopev 500689 Oct 25 2008 configure
    -r--r--r-- 1 dnascopev dnascopev 31442 Oct 25 2008 MANIFEST
    -r--r--r-- 1 dnascopev dnascopev 163659 Oct 25 2008 aclocal.m4
    -r--r--r-- 1 dnascopev dnascopev 55669 Oct 18 2008 configure.in
    -r--r--r-- 1 dnascopev dnascopev 9619 Oct 11 2008 TO-DO
    -r-xr-xr-x 1 dnascopev dnascopev 44914 Aug 30 2008 config.guess
    -r-xr-xr-x 1 dnascopev dnascopev 33704 Aug 30 2008 config.sub
    -r--r--r-- 1 dnascopev dnascopev 4019 Mar 31 2007 mk-hdr.awk
    -r-xr-xr-x 1 dnascopev dnascopev 1320 Mar 25 2007 mkdirs.sh
    -r--r--r-- 1 dnascopev dnascopev 15813 Mar 24 2007 mk-1st.awk
    -r--r--r-- 1 dnascopev dnascopev 2529 Oct 28 2006 AUTHORS
    -r--r--r-- 1 dnascopev dnascopev 4881 Apr 22 2006 convert_configure.pl
    -r--r--r-- 1 dnascopev dnascopev 9870 Apr 22 2006 README
    -r--r--r-- 1 dnascopev dnascopev 3985 Apr 22 2006 README.emx
    -r--r--r-- 1 dnascopev dnascopev 8749 Apr 22 2006 Makefile.os2
    -r--r--r-- 1 dnascopev dnascopev 3901 Jan 29 2005 Makefile.in
    -r--r--r-- 1 dnascopev dnascopev 4189 Jan 22 2005 mk-0th.awk
    -r--r--r-- 1 dnascopev dnascopev 5285 Jan 22 2005 mk-2nd.awk
    -r-xr-xr-x 1 dnascopev dnascopev 7123 Nov 29 2003 install-sh
    -r-xr-xr-x 1 dnascopev dnascopev 3038 Oct 25 2003 tar-copy.sh
    Thank you.

    Leave a comment:


  • Heisman
    replied
    I remember what we're trying to do; I think we'll get there eventually.

    A tip: with most programs in this field, once you download and untar the directory, there is usually a README or INSTALL file that will tell you what to do. If you go to the samtools directory and type "cat INSTALL", you'll see what to do. Try to install it, and then try the "pathToSamtools/samtools view -h amplicons.bam and see if it looks ok to you.

    Leave a comment:


  • cmccabe
    replied
    bed2Bam

    I have samtools installed, how do I compile it?

    Eventhough the epilepsy.bam is in a gz folder picard will reconize it?

    I am try to calculate the off-target reads and going to use HS metrics. Thank you for all your help and patience.

    Leave a comment:


  • Heisman
    replied
    If you do "head -3 epilepsy.bed | od -c" and paste the output it should be clear if the file is fine.

    Leave a comment:


  • Heisman
    replied
    I'm confused. Above you show an "amplicons.bam" file of size 16544 bytes; definitely not 0. Why do you believe something is wrong?

    Leave a comment:


  • cmccabe
    replied
    bed2Bam

    dos2unix epilepsy.bed says skipping epilepsy.bed, not a regular file. Thanks.

    Leave a comment:


  • cmccabe
    replied
    bed2Bam

    Tool: bedtools bedtobam (aka bedToBam)
    Version: v2.17.0
    Summary: Converts feature records to BAM format.

    Usage: bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome>

    Options:
    -mapq Set the mappinq quality for the BAM records.
    (INT) Default: 255

    -bed12 The BED file is in BED12 format. The BAM CIGAR
    string will reflect BED "blocks".

    -ubam Write uncompressed BAM output. Default writes compressed BAM.

    Notes:
    (1) BED files must be at least BED4 to create BAM (needs name field).

    Looks like the bed is the problem, when I did dos2unix I got the above.

    The bed:
    chr1 40539720 40539896 AMPL4669271522 . PPT1
    chr1 40542435 40542658 AMPL5154908878 . PPT1
    chr1 40544200 40544360 AMPL3675665035 . PPT1

    Thanks.

    Leave a comment:


  • Heisman
    replied
    Oh, are you trying to extract the .bam file with "gunzip" or an equivalent?

    Do you have samtools installed and compiled? If so, try to do "samtools view amplicons.bam" and you'll see what it actually looks like.

    Leave a comment:


  • cmccabe
    replied
    bed2Bam

    total 141
    -rw-rw-r-- 1 dnascopev dnascopev 16544 Jul 12 12:16 amplicons.bam
    -rw-rw-r-- 1 dnascopev dnascopev 51482 Jul 12 12:06 epilepsy.bed
    drwxrwxr-x 2 dnascopev dnascopev 1024 Jul 12 11:48 bin
    drwxrwxr-x 2 dnascopev dnascopev 3072 Jul 12 11:48 obj
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 data
    drwxr-xr-x 4 dnascopev dnascopev 1024 Jul 11 13:38 docs
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 genomes
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 scripts
    drwxr-xr-x 40 dnascopev dnascopev 1024 Jul 11 13:38 src
    -rw-r--r-- 1 dnascopev dnascopev 17988 Nov 3 2012 LICENSE
    -rw-r--r-- 1 dnascopev dnascopev 6693 Nov 3 2012 Makefile
    -rw-r--r-- 1 dnascopev dnascopev 1505 Nov 3 2012 README.rst
    -rw-r--r-- 1 dnascopev dnascopev 32293 Nov 3 2012 RELEASE_HISTORY
    drwxr-xr-x 20 dnascopev dnascopev 1024 Nov 3 2012 test

    I changed to amplicons.bed and a GZ folder with the BAM results that is 0 bytes and I get an error occurred while extracting the files. The file type in unknown so maybe that is part of it, but is 0 bytes really right?Thanks.

    Leave a comment:


  • GenoMax
    replied
    Looks like this must have already worked (looking at the date stamps).

    epilepsy.bed == Amplicons.bed

    resulted in the "Amplicons.bam" file.

    Leave a comment:


  • Heisman
    replied
    You don't have a file called "Amplicons.bed" in that folder. Where is that file? You're trying to run the command using that file but you aren't specifying the correct path to the file.

    Leave a comment:


  • cmccabe
    replied
    bed2Bam

    total 141
    -rw-rw-r-- 1 dnascopev dnascopev 16544 Jul 12 12:16 amplicons.bam
    -rw-rw-r-- 1 dnascopev dnascopev 51482 Jul 12 12:06 epilepsy.bed
    drwxrwxr-x 2 dnascopev dnascopev 1024 Jul 12 11:48 bin
    drwxrwxr-x 2 dnascopev dnascopev 3072 Jul 12 11:48 obj
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 data
    drwxr-xr-x 4 dnascopev dnascopev 1024 Jul 11 13:38 docs
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 genomes
    drwxr-xr-x 2 dnascopev dnascopev 1024 Jul 11 13:38 scripts
    drwxr-xr-x 40 dnascopev dnascopev 1024 Jul 11 13:38 src
    -rw-r--r-- 1 dnascopev dnascopev 17988 Nov 3 2012 LICENSE
    -rw-r--r-- 1 dnascopev dnascopev 6693 Nov 3 2012 Makefile
    -rw-r--r-- 1 dnascopev dnascopev 1505 Nov 3 2012 README.rst
    -rw-r--r-- 1 dnascopev dnascopev 32293 Nov 3 2012 RELEASE_HISTORY
    drwxr-xr-x 20 dnascopev dnascopev 1024 Nov 3 2012 test

    Thanks.

    Leave a comment:


  • Heisman
    replied
    Is your "Amplicons.bed" file actually gzip compressed? Otherwise this doesn't make sense. Your command line doesn't include "amplicons.bab" so I don't see why that is relevant for the command you typed. If you type "less Amplicons.bed", can you read the file, or does it tell you it may be binary format or something like that?

    Leave a comment:


  • GenoMax
    replied
    Can you post a listing of files in this folder?

    Code:
    $ ls -lt

    Leave a comment:


  • cmccabe
    replied
    Bed2Bam

    There is an amplicons.bab folder in the bedtools-2.17 directory that says gz and when I extract it An error occured extrating the files. Thank you.

    Leave a comment:

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