User: jozs2019
jozs2019 • 0
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Posts by jozs2019
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... Understood! I wrote this sed script:
sed 's|.1 |/1 |g' reads_suffixes_1.fastq
... and it seems to have worked (checking the head and tail again). Fingers crossed that assembly goes better this time, and thanks for your help! ...
written 3 months ago by
jozs2019 • 0
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... Thanks for clarifying, benv!
The first 10 lines of read 1 file:
@SRR960028.1.1 FCC0H3RACXX:5:1101:1479:2095 length=150
TNAGTGAAGGACACCGCTGGATAAAGAATAAAAGGAGATCTTGACAAAAAGAAAAAAGAGGACCTTCAAAAGTAAGGCAAGAAGAGGAGTGGTGAGTTTTCTTATAAATATTAAAAATGGGAGCTAGCAACAGTCGCTTGCCTTTTGTAT
+SRR960028.1.1 F ...
written 3 months ago by
jozs2019 • 0
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... Hello,
I'm trying to assemble contigs from a set of paired end reads, denoted as SRR960028_1.fasta and SRR960028_2.fasta. I'm running ABySS on my university's HPC facility. When I run ABySS it terminates early. The line of code itself (within the PBS file) is:
abyss-pe name=abyss_test1 k=63 in ...
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... I had a look at the file, and as you said, line 745672 was truncated in length. It was also the final line of a fastq file that should have had more lines in it. I have the feeling it was a download problem rather than anything else, it's happened in the past that my fastq files have been truncated ...
written 4 months ago by
jozs2019 • 0
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... Hello!
I'm trying to use ABySS 1.9.0 to assemble set of genomic paired end reads. I'm doing this on my university's HPC with parallel processing. In my PBS script, I use:
abyss-pe name=abyss_test1 k=63 in='SRR960028_1.fastq SRR960028_2.fastq' v=-v
Unfortunately, ABySS terminates quite quickly aft ...
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