Alignment Of Tsms Data · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Alignment Of Tsms Data

I have a data generated from Helicos using tSMS technology. I tried Bowtie it did not turn out to be good. I was reading on web and turn out SHRIMp2 may be useful as reported by authors. I was wondering: 1. Any good aligner (SE) for human ref genome with data generated by Helicos 2. What will be the best parameters to use for SHRIMP2. I can use default but may have to tweak into few for tSMS type of data.

Thanks

• 1,522 views • link

written 13.6 years ago by kanwarjag

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Cell type pathway ScRNAseq
written 6.1 years ago by kanwarjag

I am trying to find a toll/ software/ package that can identify cell specific pathways in ScRNA-seq data. I have analyzed the data and has …
Single Cell RNAseq of nuclei
written 6.4 years ago by kanwarjag

I am generating single nuclei RNAseq and was wondering is there a work flow. How different it may be from single cell RNAseq. There are …
Problem with CNVkit using samples with single-end sequenced WES
written 7.0 years ago by tangya1982 •

I have several whole-exome sequencing (WES) samples sequenced by pair-end (PE) and single-end (SE): 2 patient samples and 5 normal population samples, which were prepared …
.SMS format file
written 12.0 years ago by kanwarjag

<p>I have some sequencing data which has extension of .sms. I was wondering is there any option to convert this sms format file to fastq …
Shrimp2 On Galaxy Instance
written 13.0 years ago by kanwarjag

<p>I was wondering if there is any instance of galaxy out which has SHRIMP2 aligner? I Googled and searched but could not find one</p> <p>Thanks</p>
Chip-Seq For Mitochondrial Genes
written 13.1 years ago by kanwarjag

<p>I have a data set of chipseq and want to look for mitochondrial TF. During experiment mitochondria fractions were enriched.The data is SE 50 bp …
How To Tune Parameters When Running Shrimp2 On Longer Illumina Reads
written 13.6 years ago by kanwarjag

<p>I have been working with Miseq data (150bp) PE reads for detection of sequence variation in bacterial genome (~10Kb). I found only SHRIMP2 is giving …
Which Aligner Is Most Suited For Viral Rna-Seq Data?
written 13.7 years ago by kanwarjag

<p>I have a RNA-seq data for viral genome and would like to see expression of UT vs treated samples. I was wondering which alignment should …
The Role Of Alignment In Processing Sequencing Data
written 14.8 years ago by KCC

<p>I was reading that about MAQ and I found out that it does an alignment step. My understanding of MAQ is:</p> <p>reads --> MAQ --> …
Using Cufflinks For Rna-Seq Without Tophat/Bowtie.
written 15.1 years ago by Travis

<p>Hi, </p> <p>I was wondering if anyone has successfully used Cufflinks in combination with an aligner from another source?</p> <p>Since Bowtie doesn't make use of …