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Hi,
I want to trim EM-SEQ fastq files.
I used the same code, first for a single pair, and then for a batch.
The code for the first pair was:
trim_galore --2colour 20 --illumina -o trim --pair…
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This is a real example from a Nextseq sequencing run. The 3' end of this read is extremely low, and the read should be trimmed.
```
@test
CTTGCTCCCCTTCCTCACCGCATTCCCTAAAGCATCGCCGCCCCCGTTCGGTAAGT…
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Sage does not allow Fq to be defined with a user-supplied polynomial together with a user-supplied primitive element. However, recent (4.0.2 or newer) givaro is able to accept such input and use it.…
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Hi @biofuture
- I installed the singularity 3.8 version on ubuntu now I dont understand how to install args-oap application, I would appreciate if you could guide me in doing that. I have already …
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This is probably fixed in a branch, but presently in master switching from
vg map -f group_3.fq -i -W 500 -u 0 -t 3 graph.vg -x graph.vg.xg -g graph.vg.gcsa -n5
to
vg map **-a** -f group_3.fq…
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"mvn clean verify" returns the following failures/errors:
```
Failed tests:
BaseFramingIT.shouldEchoBinaryFrameWithPayloadLength65535:421 arrays first differed at element [65532]; expected: but was…
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Hi all,
I am using kallisto with this command:
kallisto quant -i kallisto_index --bias --genomebam --chromosomes chrm.sizes.txt --gtf ITAG3.10_gene_models.gtf -o test R2_001.tr.fq.gz R2_001.tr.fq…
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```
What steps will reproduce the problem?
$ cat test_empty_seq_line.fa
>test1
>test2
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>test3
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
…
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```
What steps will reproduce the problem?
$ cat test_empty_seq_line.fa
>test1
>test2
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>test3
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
…
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I managed to solve my issue but I wanted to bring this up especially because this might be a problem when people are trying to use SRA data which uses _1 and _2 to designate read1 and read2, respectiv…