Uninitialized value errors when running JUM_C.sh #30
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Hi Linda,
Would you send me the first 50 lines of your refFlat annotation file?
Qingqing
…On Tue, May 5, 2020 at 1:56 PM Linda Lin ***@***.***> wrote:
Hello,
I am encountering a lot of uninitialized value errors when running
JUM_C.sh and am not sure what is wrong. These include:
- in print at
/DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, line
1278 on
- Lots of things in
/media/nkaplin1/DATA5/JUM/JUM_2.0.2/final_process_MXE_output.pl lines
191-262, line 1
- $junctionID[10] in pattern match (m//) at
/DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 50, line
428/435
- in string eq at
/DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_1.pl line 53, line
428/435
- in print at
/DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_2.pl line 60
- in print at
/DATA5/JUM/JUM_2.0.2/identify_gene_name_for_JUM_output_3.pl line 45, line 2
on
I am trying to use JUM to identify IR events. More than half of the
identified IR events have gene="NONE" or even nothing (empty string?) in
the final IR output. This behavior is not exactly expected because IR
events should occur within genes, and some of these locations do map onto
genes when inspected. I am guessing that these issues might be related to
each other?
Another potential concern is that JUM is identifying fewer IR events than
perhaps expected when looking at the data. However, I'm aware that it may
have to do with the parameters I used (following the examples/suggestions).
Do you know if this could be due to the uninitialized value errors I
encountered as well, or is it only due to the parameters chosen?
I tried to follow all the directions in the manual for v2.0.2 and ran the
scripts as in the examples provided. I did not encounter any errors until
this step, and I believe my refFlat file matches the format specifications.
Would you be able to help me troubleshoot this please?
Thank you very much in advance!
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Hi Qingqing, Thank you for the reply! The first 50 lines are attached: |
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If you don't mind, could you send me the input files and the command you
used to run JUM_C.sh? I suspect it is some format issue in the input files
and would like to run it on my end to debug. The file size should not be
that large.
…On Mon, May 11, 2020 at 5:23 PM Linda Lin ***@***.***> wrote:
Hi Qingqing,
Thank you for the reply! The first 50 lines are attached:
refFlat.txt
<https://github.com/qqwang-berkeley/JUM/files/4612191/refFlat.txt>
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Hi Qingqing, I see. Sure -- are these the input files that you need? I ran JUM_C.sh using the command Thank you for your help! |
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Sorry for the late reply - was swamped the last two weeks.
The reason you were seeing this error is because when you ran JUM
previously all the chromosome names are without "chr" (check all the output
file under column "sub_junction_chr"), but in your reference file
refFlat.txt all the chromosome names are with "chr". So the script can not
find a match in chromosome names. You can simply change the chromosome name
in your refFlat.txt file and it should be fixed.
…On Wed, May 13, 2020 at 11:07 PM Linda Lin ***@***.***> wrote:
Hi Qingqing,
I see. Sure -- are these the input files that you need?
input_files.zip
<https://github.com/qqwang-berkeley/JUM/files/4625796/input_files.zip>
I ran JUM_C.sh using the command
nohup bash /DATA5/JUM/JUM_2.0.2/JUM_C.sh --Folder /DATA5/JUM/JUM_2.0.2
--Test pvalue --Cutoff 0.05 --TotalCondition1FileNum 3
--TotalCondition2FileNum 3 --REF
/DATA5/linda_JUM/Araport11_genePred_refFlat_formatted.txt > JUM_C.out &
from inside JUM_diff/FINAL_JUM_OUTPUT_pvalue_0.05/
Thank you for your help!
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No worries. Thank you for all your help! That worked well for me. I didn't realize that there was this discrepancy -- thanks for pointing it out. I still get some (although way fewer) "NONE" results in the IR output. I inspected these visually and it appears that approximately half are annotated as exons/UTRs rather than introns, while a few do correspond to introns but didn't get identified as such. Do you know why this might be? (The rest are not annotated so "NONE" seems fitting for those.) One other question for you: what is the criteria for calling "INF" for delta PSI? Thank you in advance! |
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Do you mind giving me an example of the "none" IRs that you described as "I
inspected these visually and it appears that approximately half are
annotated as exons/UTRs rather than introns, while a few do correspond to
introns but didn't get identified as such"? An igv browser shot or
something similar will be good.
"INF" can mean that in the beginning there is no intron-retained isoform
(so the basal level is zero), but after the biological change there is some
expression of the intron-retained isoform, as a result deltaPSI becomes
(IR_later - IR_before) divided by "zero", and end up with INF (infinity).
So these IR event could in fact be very interesting.
…On Thu, May 28, 2020 at 11:34 AM Linda Lin ***@***.***> wrote:
No worries. Thank you for all your help!
That worked well for me. I didn't realize that there was this discrepancy
-- thanks for pointing it out.
I still get some (although way fewer) "NONE" results in the IR output. I
inspected these visually and it appears that approximately half are
annotated as exons/UTRs rather than introns, while a few do correspond to
introns but didn't get identified as such. Do you know why this might be?
(The rest are not annotated so "NONE" seems fitting for those.)
One other question for you: what is the criteria for calling "INF" for
delta PSI?
Thank you in advance!
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Apologies for the delayed response. Here are some IGV screenshots. They are named as comment_chr_pos. (I checked the expanded gene model track and there are no alternative isoforms with introns at these sites.) I'm still a bit unclear on the "INF" results. You write in the manual that IR "deltaPSI = intron_inclusion_isoform / (intron_inclusion_isoform+intron_exclusion_isoform) (under control) - intron_inclusion_isoform / (intron_inclusion_isoform+intron_exclusion_isoform) (under treatment)." Are you saying that (intron_inclusion_isoform+intron_exclusion_isoform) would be zero under a condition? (No gene expression whatsoever? If so, would it be possible to just make the fraction zero?) I'm not sure if I'm understanding this correctly. Thank you in advance! |
Hello,
I am encountering a lot of uninitialized value errors when running JUM_C.sh and am not sure what is wrong. These include:
I am trying to use JUM to identify IR events. More than half of the identified IR events have gene="NONE" or even nothing (empty string?) in the final IR output. This behavior is not exactly expected because IR events should occur within genes, and some of these locations do map onto genes when inspected. I am guessing that these issues might be related to each other?
I tried to follow all the directions in the manual for v2.0.2 and ran the scripts as in the examples provided. I did not encounter any errors until this step, and I believe my refFlat file matches the format specifications. Would you be able to help me troubleshoot this please?
Thank you very much in advance!
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