Contig filter
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George Wang
May 9, 2016, 4:20:26 PM5/9/16
to ABySS
HI Abyss developers,
Other than the length of the contigs, are there any other filtering parameters used to count the number of contigs for N:500 in the Abyss output stat file? I found the number of N:500 of contigs in the final Abyss-stat file is different from my manual count. What I did is: first, I used
samtools faidx contig.fa
Then I counted the number of contigs whose length is greater than or equal to 500. The number does not match the one shown in the file Abyss-stat. It is slightly more than the one shown in Abyss-stat.
Thanks.
George
Other than the length of the contigs, are there any other filtering parameters used to count the number of contigs for N:500 in the Abyss output stat file? I found the number of N:500 of contigs in the final Abyss-stat file is different from my manual count. What I did is: first, I used
samtools faidx contig.fa
Then I counted the number of contigs whose length is greater than or equal to 500. The number does not match the one shown in the file Abyss-stat. It is slightly more than the one shown in Abyss-stat.
Thanks.
George
Shaun Jackman
May 9, 2016, 5:29:54 PM5/9/16
to ABySS
Hi, George. `abyss-fac` does not count Ns toward the 500 bp, and `samtools faidx` counts all symbols. I've added you question to the FAQ.
Cheers,
Shaun
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