diff --git a/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt b/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt
index 2fd57bf1acdc526ec18cb03867db8bfc87042532..a61288bdab06243091160a30c153200f36cb1766 100644
--- a/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt
+++ b/misc-scripts/xref_mapping/docs/running_the_xref_pipeline.txt
@@ -91,6 +91,9 @@ Good docs can be found at
https://www.ebi.ac.uk/seqdb/confluence/display/ENS/Importing+LRGs+into+Ensembl
which comes down to doing the following :-
+Check that the LRG modules are added to perl5lib
+so for my instance I set
+setenv PERL5LIB ${PERL5LIB}:/nfs/users/nfs_i/ianl/LRG/code/modules
perl scripts/import.lrg.pl -verbose -do_all -host ens-staging -port
3306 -user rw -pass password -core homo_sapiens_core_65_37
@@ -116,13 +119,10 @@ perl scripts/import.lrg.pl -verbose -do_all -host ens-staging -port
homo_sapiens_cdna_65_37 -vega homo_sapiens_vega_65_37 -rnaseq
homo_sapiens_rnaseq_65_37 -verify >& verify.OUT
-need to add modules to perl5lib to know where to find the modules
-so for my instance i set
-setenv PERL5LIB ${PERL5LIB}:/nfs/users/nfs_i/ianl/LRG/code/modules
-If the cdna databses is not yet ready then remove the "-cdna
+If the cdna databases are not yet ready then remove the "-cdna
homo_sapiens_cdna_65_37" bit and continue but let who ever is building
-this database that you are doing the LRGs so that they get the same
+this database know that you are doing the LRGs so that they get the same
data.
@@ -130,8 +130,7 @@ data.
Run the parsing
---------------
-More detailed instructions can be found in the FAQ.txt and
-
+More detailed instructions can be found in the FAQ.txt,
but basically you should cd to where you want the files to be downloaded to
and run the following;-
@@ -163,7 +162,7 @@ Explanation of the output:-
> -dbname ianl_human_xref_65 -species human -stats -
> create -force
-Tells us what options were used when the parser script was ran.
+Tells us what options were used when the parser script was run.
> ----{ XXXX }-----------------------------------------------------------------
@@ -325,7 +324,7 @@ to do next
>No alt_alleles found for this species.
-only for human do we inport the alt_alleles
+only for human do we import the alt_alleles
>Dumping xref & Ensembl sequences
@@ -347,7 +346,7 @@ exist they will not be re dumped.
>already processed = 0, processed = 734, errors = 0, empty = 0
This is information on the mapping of the fasta files using exonerate. Check that
-the errors are 0 else one of the mapping went wrong.
+the errors are 0 else one of the mappings went wrong.
>Could not find stable id ENSDART00000126968 in table to get the internal id hence
@@ -367,7 +366,7 @@ this is not a problem.
> ZFIN_ID
Priority xrefs are those xrefs where we get the data from more than one place.
-These will have prioritys which tell us which is better so the best ones are
+These will have priorities which tell us which is better so the best ones are
chosen at this point.
@@ -403,7 +402,7 @@ highest and Translation the lowest.
>DBASS3 moved to Gene level.
>DBASS5 moved to Gene level.
-Some sources are considered to belong to genes but maybe mapped to transcripts or
+Some sources are considered to belong to genes but may be mapped to transcripts or
translations so we move these now to the gene.
@@ -416,8 +415,8 @@ translations so we move these now to the gene.
> wu:fj89a05 (left as ZFIN_ID reference but not gene symbol)
For some sources (HGNC in human, MGI in mouse and ZFIN_ID in zebrafish) we only
-want to have one reference per gene so using things like their prioritys, %id
-mapping values etc we try to find the best one and remove the others. If we cannot
+want to have one reference per gene so using things like their priorities, %id
+mapping values etc. we try to find the best one and remove the others. If we cannot
find a best one then all are kept.
@@ -491,7 +490,7 @@ So we report the number and type of xrefs that are loaded.
>Setting Transcript and Gene display_xrefs from xref database into core and
> setting the desc
-In the official naming routine which mouse, human and zebrafish run we set
+In the official naming routine which mouse, human and zebrafish run, we set
the display_xrefs and descriptions.
@@ -513,8 +512,8 @@ Used for checking/debuging mainly.
> RFAM 9
>6437 gene descriptions added
-For those that the official naming routine could not set we now add display_xrefs
-and decriptions. NOTE: the higher the number ther greater the priority for naming.
+For those that the official naming routine could not set, we now add display_xrefs
+and descriptions. NOTE: the higher the number the greater the priority for naming.
>xref_mapper.pl FINISHED NORMALLY