mpizzagalli777
commented
5 months ago Just to clarify, I am actually able to run through all of the following scripts, until the final commands max_speed.py step. All other steps worked correctly.
python $teproflib/rmskhg38_annotate_gtf_update_test_tpm.py \
$wkdir/${sample}_alignment/${sample}_Aligned.sortedByCoord.out.gtf \
$teproflib/arguments.txt
python $teproflib/annotationpmprocess.py \
$wkdir/${sample}_TEProf2/${sample}_Aligned.sortedByCoord.out.gtf_annotated_filtered_test_all
Rscript $teproflib/aggregateProcessedAnnotation.R $wkdir/${sample}_TEProf2/${sample}_Aligned.sortedByCoord.out.gtf_annotated_filtered_test_all_c \
-k yes -a $teproflib/arguments.txt
mkdir $wkdir/filterreadstats
python $teproflib/commandsmax_speed.py $wkdir/${sample}_TEProf2/filter_combined_candidates.tsv $wkdir/${sample}_alignment/The output of head filter_combined_candidates.tsv -n 2 is as follows:
STRG.9484.3 None None None None None None None None None None None None Yes protein_coding PTN chr7 137343439 137343865 exon 1 chr7;137254971;137254973 137227341 137343865 137254859,137254974,137343439,137343865,137254975,137343438,137253638,137254858,137253464,137253637,137251230,137251391,137228076,137251229,137251392,137253463,137227341,137228075 ENST00000348225.6 chr7 137345817 137227352 -,chr7,137228075,137227352,137251391,137251230,137253637,137253464,137254974,137254859,137343699,137343439,137345130,137345066,137345817,137345647 None chr7 137345640 137346278 MER41B 4398 - - 119.900139 6.754386 22.363449 888.963501 165.807068 250.236212 SRR7820938_Aligned.sortedByCoord.out 1 0 0.134876335040892 0.0893693555431538 LTR ERV1 MER41B_137345640_None_None_None_PTN_exon_1_137227341_SRR7820938_Aligned.sortedByCoord.out 171 137345131 137345646 MER41B_137345640_None_None_None_PTN_exon_1_137227341 STRG.59.2 protein_coding ATAD3B chr1 1477351 1478643 intron 2 chr1;1471885;1471887 1471769 1496202 1487863,1487914,1495485,1496202,1471769,1472089,1490672,1495484,1490257,1490424,1479109,1480866,1487915,1489203,1486110,1486235,1490563,1490671,1485016,1485171,1478644,1478745,1478746,1479048,1486236,1486543,1482304,1482544,1477274,1477350,1486669,1487862,1485172,1485781,1482615,1485015,1482138,1482303,1485839,1486109,1482545,1482614,1479049,1479108,1490425,1490562,1472090,1477273,1486544,1486668,1489204,1489274,1489275,1490256,1485782,1485838,1480867,1480936,1477351,1478643,1480937,1482137 ENST00000308647.7 Yes protein_coding ATAD3B chr1 1479049 1479108 exon 4 chr1;1471885;1471887 1471769 1496202 1487863,1487914,1495485,1496202,1471769,1472089,1490672,1495484,1490257,1490424,1479109,1480866,1487915,1489203,1486110,1486235,1490563,1490671,1485016,1485171,1478644,1478745,1478746,1479048,1486236,1486543,1482304,1482544,1477274,1477350,1486669,1487862,1485172,1485781,1482615,1485015,1482138,1482303,1485839,1486109,1482545,1482614,1479049,1479108,1490425,1490562,1472090,1477273,1486544,1486668,1489204,1489274,1489275,1490256,1485782,1485838,1480867,1480936,1477351,1478643,1480937,1482137ENST00000308647.7 chr1 1477849 1496200 +,chr1,1477849,1478745,1479049,1479108,1480867,1480936,1482138,1482303,1482545,1482614,1485016,1485171,1485782,1485838,1486110,1486235,1486544,1486668,1487863,1487914,1489204,1489274,1490257,1490424,1490563,1490671,1495485,1496200 chr1,1478746,1479048,chr1,HAVANA,intron,1478746,1479048,.,+,.,gene_id ENSG00000160072.19; transcript_id ENST00000472194.6; gene_type protein_coding; gene_status KNOWN; gene_name ATAD3B; transcript_type retained_intron; transcript_status KNOWN; transcript_name ATAD3B-002; intron_number 1; exon_id ENSE00001943609.1; level 2; transcript_support_level 1; havana_gene OTTHUMG00000000577.5; havana_transcript OTTHUMT00000001370.3;,transcript_id ENST00000472194.6,14 chr1 1477677 1478003 AluSp 2149 - + 94.325249 251.117706 17.59329 94.325249 17.59329 18.252984 SRR7820938_Aligned.sortedByCoord.out 1 0 1 0.963858292978288 SINE Alu AluSp_1477677_ATAD3B_intron_2_ATAD3B_exon_4_1471769_SRR7820938_Aligned.sortedByCoord.out 897 1478746 1479048 AluSp_1477677_ATAD3B_intron_2_ATAD3B_exon_4_1471769
When I run commandmax_speed.py, the error is as follows: File "..../commandsmax_speed.py", line 35, in
Do you see what the issue might be?
So sorry for the long follow up! Just wanted to provide some more context
Hi, I have a question that was mostly answered elsewhere (#11). However, I was wondering if it would be possible to update the input files in order to get around this issue. In other words, if I followed the steps you outlined in the README, and create the new reference files with my version of gencode would the pipeline work? Or is it a requirement to use the v25 version of gencode?
Thanks so much!