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If I understood correctly, I cannot use lumpy express on a merged bam file with different RGs.
So, I have to have separate bam files (aligned with bwa mem -M -R ) and do this on each:
* Sort & I…
JJBio updated
4 years ago
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Comparing a test run from 201223 and 200224 there is a slight difference in the output. The first one detect 91 reads towards Leptospira yasudae. The second run detects 90. There is no difference in t…
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### Description
Maybe I'm missing something, but how does achieve parallelism during a `flat_map` operation? Certain `flat_map` ops can generate multiple output rows from a single input row in a comp…
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So I'm trying to run clear_quant on a RNA-seq file I obtained online (Ribo-), but I cannot seem to move past the following error:
> ###Parameters:
> Namespace(bowtie1='/home/nilu/Alignment_db/base…
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Here is the command that is run:
```
tophat -p 7 --fusion-search -o SecondTry FusedReference M_05_66.1 M_05_66.2
```
Here is the output:
```
Warning: --fusion-search with Bowtie2 may not wo…
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Currently there is no information on the correct (true) position of the reads. To avoid the uncertainty of the mapping step SAM output for simulated mapped reads would be really nice.
best,
FGV
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I want to use the postgres interval data type. Unfortunately is the value not written to the database. While debugging the query mapping, the build query is correct. But after execution there is nothi…
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Dear Tobias:
I have part of the data 4SU labeled mRNA library built using the total RNAseq. How do I use slamDunk to analyze them. Same issue #89
By the way, what is the mismatch of the slamdunk…
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When mapping multiple `fastq` using `--readFilesIn` together with `--outSAMattrRGline`, the `RG` tag is added to the SAM header and all reads.
However, when mapping with manifest using `--readFiles…
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May I ask why the value of "Reads Mapped to Genome" is higher than "Valid Barcodes" when I provided a whitelist of barcodes for analysis using STARsolo software? How to use STARsolo to ensure that the…