Samarpan Hospital and Research Center

Gene1	Gene2	Fusion Copies(Seracare)	repA_Auto	repA_Manual	repB_Auto	repB_Manual	repC_Auto	repC_Manual	repD_Auto	repD_Manual	repE_Auto	repE_Manual	repF_Auto	repF_Manual	repG_Auto	repG_Manual	repH_Auto	repH_Manual
PAX8	PPARG	1621	7	17	6	9	7	6	4	11	8	14	5	13	6	23	8	4
EML4	ALK	1148	10	14	14	10	11	11	12	3	7	14	9	18	9	18	14	2
CD74	ROS1	955	9	9	14	16	15	11	6	17	7	14	19	15	8	19	10	9
FGFR3	TACC3	919	7	20	10	12	11	11	6	7	14	18	21	9	2	12	17	6
NCOA4	RET	899	3	10	7	14	7	13	5	6	3	0	9	4	7	9	9	1
EGFR	SEPT14	828						3
SLC45A3	BRAF	828	1	8	11	8	17	8	9	11	5	5	4	23	4	20	11	8
ETV6	NTRK3	798	7	14	6	16	20	11	7	9	13	13	9	21	16	19	10	4
SLC34A2	ROS1	634	2	2	3	9	7	3	1	6	1	5	3	1	1	10	6	3
FGFR3	BAIAP2L1	615	19	16	11	19	7	24	10	14	11	4	16	14	9	21	4	8
LMNA	NTRK1	605	1	1				6	3		2	3					2	1
TPM3	NTRK1	596	10	11	16	20	8	13	10	13	12	17	5	16	7	28	18	6
KIF5B	RET	520	10	9	6	3	10	14	6	11	7	10	2	7	8	15	7	4
TMPRSS2	ERG	516	1	1		5	1		2	1	1	1	4		4	3	1	2

Research ID

A comprehensive NGS data analysis pipeline

Here is the pipeline I wrote which uses snakemake to manage jobs and run >80 different tool on Exome/Panle/Whole genome/RNASeq/Methylseq datasets


https://github.com/patidarr/ngs_pipeline

igv session file example

xml file example for igv_session

Browser based Shell connection

Most of the time I need to login to the server to submit the jobs or check the status of the running job and for programming, at my desk I have MTPPuTTY for this purpose. But what if you are at vacation and want a quick look at the jobs you are running or submit a new job. I started googling and found what I was looking for "A web browser based secure shell connection extension for Google chrome". 


Install it and give it a shot, its pretty impressive. you can customize it (tools-> Extensions->options in secure shell extension).

File checking in Perl

A list of checking you can perform on a file in perl
Commanly used checks are in Bold Font
-r      File is readable by effective uid/gid.
-w      File is writable by effective uid/gid.
-x      File is executable by effective uid/gid.
-o      File is owned by effective uid.
-R      File is readable by real uid/gid.
-W      File is writable by real uid/gid.
-X      File is executable by real uid/gid.
-O      File is owned by real uid.
-e      File exists.
-z      File has zero size (is empty).
-s      File has nonzero size (returns size in bytes).
-f      File is a plain file.
-d      File is a directory.
-l      File is a symbolic link.
-p      File is a named pipe (FIFO), or Filehandle is a pipe.
-S      File is a socket.
-b      File is a block special file.
-c      File is a character special file.
-t      Filehandle is opened to a tty.
-u      File has setuid bit set.
-g      File has setgid bit set.
-k      File has sticky bit set.
-T      File is an ASCII text file (heuristic guess).
-B      File is a "binary" file (opposite of -T).
-M      Script start time minus file modification time, in days.
-A      Same for access time.
-C      Same for inode change time (Unix, may differ for other platforms)