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Old 11-19-2018, 04:06 AM   #1
loost250
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Location: china

Join Date: Nov 2018
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Default cutadapt or trim galore on color space data.

1. I download the sra files and get the .qual & .csfasta.
2. get the fastq file using solid2fastq.py.
3. running fastqc on the fastq indicating high content of solid smallRNA adapter.
4. tried both cutadapt and trim galore! on the fastq file:In read named 'SRR1510896.1 1_16_1976_F3': length of quality sequence (50) and length of read (51) do not match
step 4 was run on galaxy!
how can I solve the problem? am I using the wrong trim software?
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Old 11-20-2018, 02:49 AM   #2
fkrueger
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Location: Cambridge, UK

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Default

Cutadapt can deal with your data, this is taken from the Cutadapt help:

Code:
 Colorspace options:
    -c, --colorspace    Enable colorspace mode
    -d, --double-encode
                        Double-encode colors (map 0,1,2,3,4 to A,C,G,T,N).
    -t, --trim-primer   Trim primer base and the first color
    --strip-f3          Strip the _F3 suffix of read names
    --maq, --bwa        MAQ- and BWA-compatible colorspace output. This
                        enables -c, -d, -t, --strip-f3 and -y '/1'.
    -z, --zero-cap      Change negative quality values to zero. Enabled by
                        default in colorspace mode since many tools have
                        problems with negative qualities
    --no-zero-cap       Disable zero capping
Trim Galore does not allow using the colour space switch, so please use Cutadapt instead.
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