huangyh09 / diceseq Goto Github PK

Hello Huang,

I use diceseq to count reads from RNA-seq data with total library.
But, I do not understand the mean of output file (xx.dice).
Could you show me the mean of every column?

BWT, if I use parameter of "--add_premRNA", could it work for poly(A) captured mRNA-seq?

diceseq -a $anno_file -s $sam_file -t 1,5 --add_premRNA=True -o xx

gene_id transcripts count_T1.0 ratio_T1.0 95CI_T1.0 count_T5.0 ratio_T5.0
95CI_T5.0
YDL219W YDL219W,YDL219W.p 76 0.348 0.132:0.557 74 0.589 0.383:0.777
YDL191W YDL191W,YDL191W.p 136 0.553 0.410:0.680 116 0.807 0.722:0.870
YDL136W YDL136W,YDL136W.p 129 0.553 0.350:0.698 123 0.763 0.644:0.851
YDL130W YDL130W,YDL130W.p 78 0.312 0.164:0.460 64 0.480 0.322:0.646

The upgraded numpy (from v1.13) is not compatible with diceseq. Please use older version of numpy, e.g., by

pip install -I numpy==1.12.0

Hello, after running just fine for hours DICESeq failed with this error.
[DICEseq] running diceseq for 21458 genes with 25 cores...
[DICEseq] [=========-----------] 43.8% done in 86868.4 sec.Traceback (most recent call last):
File "/users/sk1350/.conda/envs/diceseq_env/bin/diceseq", line 8, in
sys.exit(main())
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/diceseq.py", line 239, in main
sort_dice_file(out_file+".dice", tran_ids)
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/utils/run_utils.py", line 45, in sort_dice_file
fid.writelines(delimiter.join(list(data[i+1,:])) + "\n")
TypeError: unsupported operand type(s) for +: 'NoneType' and ‘int'

Hello I am trying to look at changes in isoform expression between different Xenopus development stages. I have used HISAT for alignment and the .gtf file is from Ensembl:

my_sam_list=SRR489459.sorted.bam---SRR489460.sorted.bam---SRR489462.sorted.bam
diceseq -a Xenopus_tropicalis.Xenopus_tropicalis_v9.1.98.gtf -s $my_sam_list -t 6,8,10 -o dice_seq_output.txt

And it gave me this error:
……………
Cannot fetch reads in region: KV466212.1:259-1340
Cannot fetch reads in region: KV467030.1:200-961
Cannot fetch reads in region: KV467044.1:156-274
Cannot fetch reads in region: KV467044.1:420-528
Cannot fetch reads in region: KV467044.1:671-789
Cannot fetch reads in region: KV467044.1:935-1053
Cannot fetch reads in region: MT:1082-2716
Traceback (most recent call last):
File "/users/sk1350/.conda/envs/diceseq_env/bin/diceseq", line 8, in
sys.exit(main())
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/diceseq.py", line 239, in main
sort_dice_file(out_file+".dice", tran_ids)
File "/users/sk1350/.conda/envs/diceseq_env/lib/python2.7/site-packages/diceseq/utils/run_utils.py", line 41, in sort_dice_file
idx = id_mapping(tran_ids, data[1:, 0])
IndexError: too many indices for array

Hello, Prof Huang! I'm sorry to disturb you. I have a question to ask you. I have made some errors while installing diceseq, I think I should be installed successfully, but when running the code there is the following error. I'm not sure if it is my python environment or something else, here is my installation method:
conda create -n dicePy2 python=2.7 numpy==1.15.4 scipy==1.1.0 matplotlib==2.2.3 pysam==0.15.2
source activate dicePy2
and false content:
dice-count -a dice_count.gtf -s SRR5582776sorted.bam -o SRR5582776dice.txt --junction
Welcome to dice-count!
loading annotation file... Done.
Traceback (most recent call last):
File "/home/MK/anaconda3/bin/dice-count", line 8, in
sys.exit(main())
File "/home/MK/anaconda3/lib/python3.7/site-packages/diceseq/dice_count.py", line 132, in main
_map_num = np.loadtxt(pysam.idxstats(sam_file), "str")[:,2]
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", line 926, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 262, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "/home/MK/anaconda3/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 618, in open
raise IOError("%s not found." % path)
OSError: I 230218 4139798 0
II 813184 16449284 0
III 316620 3758010 0
IV 1531933 19246328 0
V 576874 15693472 0
VI 270161 2536644 0
VII 1090940 18417732 0
VIII 562643 8431090 0
IX 439888 3765040 0
X 745751 10401514 0
XI 666816 8530514 0
XII 1078177 30091252 0
XIII 924431 12279986 0
XIV 784333 8578248 0
XV 1091291 15079578 0
XVI 948066 14969088 0
Mito 85779 928264 0

• 0 0 0
  not found.