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It seems that "penalty" for soft clip, which is specified by the `-L` argument is "reward" rather than "penalty". More specicailly, given the example below:
reference file is
```
>ref
ACTGGCAT…
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i am trying to align RNA Seq data with bowtie2 after making index, but getting this error
**bowtie2-align exited with value 1**
$ bowtie2 -x /home/dataset/Desktop/Bow_Tie2_Index -1 /home/dataset/Gr…
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Hi,
I am trying to utilize seqtk in order to convert quality score encoding of raw FASTQ files from illumina 1.5 to Sanger / illumina 1.9
my command line was:
seqtk seq -VQ64 inputfile-illumina1.5…
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Greetings,
When I run the following command:
`python ./VaST-master/VaST/preprocessing.py test /media/bjarne/SSD1/Taro_Flashdrive/ /media/bjarne/SSD1/Taro_Flashdrive/Taro1.fq_var_SiteMatrix.txt -…
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https://github.com/Snitkin-Lab-Umich/scripts/blob/32b965c6a25fd8f26de5b8044b37e06597104a42/variant_matrix_qc.R#L125
Per lab meeting discussion on March 29
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From the [tutorial](http://kevlar.readthedocs.io/en/stable/quick-start.html) with this command:
```
kevlar simplex \
--case proband.fq.gz --case-min 6 \
--control mother.fq.gz --control …
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On the samtools 1.3 release fastq doesnt add a /1 or /2 to the end of the read names in the output fastqs. So both of these command give the same result, when the -n parameter should toggle it off an…
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Hey! I'm trying to build and push (to gitlab registry) my project in `quay.io/buildah/stable` build container.
The build works fine when i do:
`devcontainer build --docker-path buildah --workspace-…
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Hi!
I am trying to BSMAP using following command line:
"BSMAPz/bsmapz -a /media/waqas/30004AFD3CB35412/All_Data/WGBS-Seq/epiRIL-368/Raw/epiRIL-368_QC_Reads_WGBS/Epiril368_4_C_R1_L001_R1_val_1.fq.g…
CS791 updated
4 years ago
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Hello, I feel like I'm missing something obvious. I have downloaded the demo data from Dropbox making sure I have the recommended folder structure of acquisition and analysis. My goal is to test my sc…