![]() Input plain text file containing the path of BAM file ( s ). Input several BAM files ( separated by "," ). It does not report exon and intron level count.ġ. FPKM.py will report “raw fragment count”, “FPM” and “FPKM” for each gene. This happened when reads were clipped and spliced mapped simultaneously.Īdd FPKM.py. ![]() “bam_stat.py” prints summary statistics to STDOUT.įix bugs in “insertion_profile.py”, “clipping_profile.py”, and “inner_distance.py “įix bug in “junction_annotation.py” in that it would report some “novel splice junctions” that don’t exist in the BAM files. Remove “RPKM_count.py” as it generates erroneous results especially for longer reads. bx-python and pysam will be installed automatically if they haven’t been installed before.įix a bug in “read_quality.py” that does not return results if input file containing less than 1000 reads. #Download splice for mac installUsers could install RSeQC using pip: pip install RSeQC. Two dependency packages bx-python and pysam are not shipped with RSeQC starting from v2.6.4. Please use previous versions (v2.6.5 or older) if you are using Python2. Junctions detected from the junction_annotation.py will be converted into Interact format file, which can be uploaded into UCSC genome browser for visualization. ![]() ![]() Add FPKM-UQ.py to calcualte HTSeq count, FPKM and FPKM-UQ values defined by TCGAįPKM-UQ.py could exactly reproduce TCGA FPKM-UQ values, if you use TCGA BAM file (or follow TCGA RNA-seq alignment workflow to generate your own BAM file), the GDC.h38 GENCODE v22 GTF file and the GDC.h38 GENCODE TSV file. ![]()
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