looking for support

[Dr A. Ismail]

Dear all, kindly I faced a problem when I correct the GC bias, by using
correctGCBias after computeGCBias.
ALthough, the GC metrics improved comparing with no GC correction.
However, when I try to build the Tag ALign file using the following
command line;
$ samtools sort -n -O BAM 0.5h_1gc_corrected.sorted.bam | bedtools
bamtobed -i stdin -bedpe | awk 'BEGIN{FS="\t";OFS="\t"}{print
$1,$2,$6,"N",$8,$9}' | gzip > 0.5h_1_sorted.rmDup.q20.tagAlign.gz


I got a lot of these waring messages on the screen;
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:17094:5517 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:17262:16944 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:17844:15877 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:17844:15877_2 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:18013:11689 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:18013:11689_2 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:18417:9557 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:18774:4427 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:19775:10816 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:19775:10816_2 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:20006:16940 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:21909:1999 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:22875:19353 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766_2 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766_3 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766_4 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766_5 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:23850:4766_6 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:24445:3436 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:24924:14387 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21605:26256:14163 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:1425:12113 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:1680:8482 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:1680:8482_2 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:3441:18673 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:3707:2579 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:3707:2579_2 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:3767:4045 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:6005:7299 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:6100:9187 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296 is marked
as paired, but its mate does not occur next to it in your BAM file.
Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_2 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_3 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_4 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_5 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_6 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_7 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_8 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.
*****WARNING: Query NB501178:367:HYTHGBGX7:4:21606:7582:15296_9 is
marked as paired, but its mate does not occur next to it in your BAM
file. Skipping.


When I use the same codes but with no GCBias correction, I got no
warning

I am looking for your help and support
Best regards
Ahmed

[Devon Ryan]

The tagAlign format hasn't been used in many years, I suggest you use
a more modern peak caller that accepts BAM or at least SAM files.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

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