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Hi,
first of all, I really like using Salmon for RNAseq quantification. I have a very special problem. We are working with experimental conditions in which transposons get activated and highly expr…
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Hi,
I have two libraries that I am having problems with the bacteria_tradis mapping for. I have used cutadapt to trim the transposon (and adapters) from the reads and selected only the reads that c…
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Spec:
1. Load all FlyBase features with the following types:
```SQL
SELECT f.uniquename AS fbid, typ.name as ftype; FROM feature f
JOIN cvterm c on f.type_id=c.cvterm_id
…
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Dear Bo Han,
In one of my analyses, the *.transposon.unique.pdf file is never generated by `piPipes chip`
I could trace the problem in the error log:
```
no data in region FBgn0046701_Penelope:0-80…
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Hi Weilong,
Thanks for putting BSseeker2 up, this is a just wonderful tool!
Comparing the BAM files generated by BSseeker2 starting from paired-end reads, with the ones generated with another prog…
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Hi,
I'm almost new in programming and I'm using one of compute canada servers to do RNA-seq data analysis. I downloaded and unzipped the latest version of STAR (2.7.5b) and I'm gonna add it to my …
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Dear Dr.Han,
I have a problem about mapping when I used the small RNA pipeline. I follow the "install" and install the genome. But I failed in mapping and I don't know how to solve it.
Here is my…
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Hi thank you so much for this tool.
I'm writing again because I cant manage to make it run on my real data.
I create a conda env with Python2.7, I notice that on previous issues gawk was necessary…
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Adapter trimming
Running Collapse
Reading from file ./trimmed/HI.3965.005.RPI1.1-1_R1.fastq.gz
Processing reads
Original number of reads: 16651798
collapsed number of reads: 732060
Mapping to hg…
frimz updated
5 years ago
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If the extend_read value is smaller than certain reads, those should not be affected. Right now, those are shrunk.
An appropriate test is commented out at the end of the test.metagene_extend_reads …