Question: Strand specific pair end sequencing
0
gravatar for Bioinfonext
2.5 years ago by
Bioinfonext160
Korea
Bioinfonext160 wrote:

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

rna-seq • 3.2k views
ADD COMMENTlink modified 2.5 years ago by h.mon27k • written 2.5 years ago by Bioinfonext160
1

RSeQC infer_experiment.py

ADD REPLYlink written 2.5 years ago by iraun3.6k

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

ADD REPLYlink written 2.5 years ago by Bioinfonext160

pip install RSeQC should take care of installing other python modules required. You can do pip install bx now.

ADD REPLYlink written 2.5 years ago by h.mon27k

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]#

ADD REPLYlink written 2.5 years ago by Bioinfonext160

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

ADD REPLYlink written 2.5 years ago by Bioinfonext160
1
gravatar for h.mon
2.5 years ago by
h.mon27k
Brazil
h.mon27k wrote:

Do you know the library prep kit? Was it Truseq stranded mRNA? If yes, it is a dUTP protocol, so it is fr-firststrand - read more here.

ADD COMMENTlink written 2.5 years ago by h.mon27k

we use this kit for library preparation:

Ovation RNA-Seq Systems 1–16 for Model Organisms PART NOS. 0351 ARABIDOPSIS kit

ADD REPLYlink written 2.5 years ago by Bioinfonext160
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