I have a strand-specific pair-end Illumina sequencing data. I am not able to understand which option to use in the different software. For each library I have two files: R1 and R2 and I am not sure about forward strand and reverse strand.
I have mapped these R1 and R2 fq files to genome. Please suggest how should I determine which option should I use for Trinity, Hisat2, and StringTie.
Is there any tool to find information about strand-specific pair-end reads?
Trinity:
--SS_lib_type <string> :Strand-specific RNA-Seq read orientation.
if paired: RF or FR,
hISAT2-Paired-end: --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
StringTie --rf assume stranded library fr-firststrand --fr assume stranded library fr-secondstrand
Thanks
RSeQC infer_experiment.py
Thanks,
I getting error when running RSeQC script. please suggest why I am getting error:
[root@psgl software]# /home/yog/software/RSeQC-2.6.4/scripts/infer_experiment.py Traceback (most recent call last): File "/home/yog/software/RSeQC-2.6.4/scripts/infer_experiment.py", line 49, in <module> from bx.bitset import * ImportError: No module named bx.bitset
Is it related to installation. I am using CentOS platform.
Command line which I used for installation:
[root@psgl RSeQC-2.6.4]# python setup.py install
pip install RSeQC
should take care of installing other python modules required. You can dopip install bx
now.still getting error
[root@psgl software]# cd RSeQC-2.6.4/ [root@psgl RSeQC-2.6.4]# pip install bx bash: pip: command not found... [root@psgl RSeQC-2.6.4]#
Please suggest the library type:
output result of RSeQC:
This is PairEnd Data Fraction of reads failed to determine: 0.0196 Fraction of reads explained by "1++,1--,2+-,2-+": 0.9360 Fraction of reads explained by "1+-,1-+,2++,2--": 0.0444
Wheather is fr-firststrand --fr assume stranded library fr-secondstrand for StringTie
What about HISAT2 and Trinity?
Thanks