pennseq's Introduction
# Copyright (c) 2013, Yu Hu and Mingyao Li (Perelman School of Medicine, University of Pennsylvania) # All rights reserved. ######################### UPADATES: # 01/11/2017: Application of Pysam module was added REQUIREMENTS: (i) Python v2.X (ii) Pysam (iii) Indexed BAM file as input #####################STEP(1)######################### The perl script "PreProcess.pl" will give the compatible matrix of isoforms for each gene. USAGE OF preprocess.pl: "./PreProcess.pl -r RefSeqAnnotation -o Outputfile" The RefSeqAnnotation file is downloaded from UCSC Genome Browers. The format is as follows -------------------------------------------------------------------------------------------- #bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds id name2 cdsStartStat cdsEndStat exonFrames 774 NM_001251984 chr1 + 24828840 24863510 24859578 24861767 4 24828840,24857707,24859572,24861582, 24828953,24857881,24859744,24863510, 0 RCAN3 cmpl cmpl -1,-1,0,1, 774 NM_001251979 chr1 + 24828840 24863510 24840862 24861767 5 24828840,24840803,24857707,24859572,24861582, 24828953,24841057,24857881,24859744,24863510, 0 RCAN3 cmpl cmpl -1,0,0,0,1, 774 NM_001251977 chr1 + 24829386 24863510 24840862 24861767 5 24829386,24840803,24857707,24859572,24861582, 24829607,24841057,24857881,24859744,24863510, 0 RCAN3 cmpl cmpl -1,0,0,0,1, 774 NM_001251981 chr1 + 24829386 24863510 24840862 24861767 4 24829386,24840803,24859572,24861582, 24829607,24841057,24859744,24863510, 0 RCAN3 cmpl cmpl -1,0,0,1, --------------------------------------------------------------------------------------------- -r ---RefSeqAnnotation file -o ---The file name that you want to save the results; it will be the input file for "pennseq.pl" The file "RefSeqAnnotation_ECE1_example" is an example of RefSeqAnnotation. The file "ISOFORM_Compatible_Matrix_example" is an example of the processed annotation by preprocess.pl #####################STEP(2)######################### The Python script "PennSeq.py" will calculate the relative abundance for each isoform. USAGE OF pennseq.pl: "python PennSeq.py -ref ISOFORM_Compatible_Matrix -bam Indexed_BAM_File -out Output_Result_FILE" -bam ---Indexed_BAM_File is the mapping result file generated by mapping tools such as TopHat. -ref ---ISOFORM_Compatible_Matrix is from the output of preprocess.pl -out ---The file name that you want to save the results The data file "BAM_example.sorted.bam" is an example Indexed Bam File. The file "Output_Result_FILE" is an example of results file. ------------------------------------------------------------------------------------- Contact inforamtion For more information, addtional data and scripts (such as the simulation and plot codes), bug reports and comments, please contact Yu Hu via [email protected].
pennseq's People
pennseq's Issues
Error in getCigarStringInformation
To Whom It May Concern,
When generating isoform relative abundances for a dataset using your PennSeq, I got the following error:
using PennSeq, I got the following error:
Traceback (most recent call last):
File "~/program/PennSeq/PennSeq.py", line 289, in
test1.aln.sam.txt
cigarMatchRead1, cigarNumberRead1, cigarMatchInfoCount1, cigarNumberInfoCount1 = getCigarStringInformation(readCigar, readName, 1)
File "~/program/PennSeq/PennSeq.py", line 24, in getCigarStringInformation
cigarNumberRead[cigarMatchInfoCount] = int(splitCigar[i])
ValueError: invalid literal for int() with base 10: '92=1'
The dataset (a sam file) was attached.
Thanks a lot for your help.
Max
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