User: jozs2019
jozs2019 • 10
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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 14 months ago by
jozs2019 • 10
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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 14 months ago by
jozs2019 • 10
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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 15 months ago by
jozs2019 • 10
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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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