# ShortBRED **URL:** https://forum.biobakery.org/c/microbial-community-profiling/shortbred/24.md?page=1 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 2 --- ## [Which file contains the final results?](https://forum.biobakery.org/t/which-file-contains-the-final-results/3114)
**Author:** [@plicht](https://forum.biobakery.org/u/plicht)\ **Replies:** 0\ **Last updated:** [February 10, 2022, 5:40pm UTC](https://forum.biobakery.org/t/which-file-contains-the-final-results/3114 "2022-02-10T17:40:56Z")
Given the user manual I am a bit confused which file contains final ready-to-use RPKM counts and which file contains raw, unnormalized counts. If (“wgs” or “fullgenome”)\_results.tab contains raw counts, why do I have fl… --- ## [Handling Paired-End Reads in ShortBRED](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878)
**Author:** [@plicht](https://forum.biobakery.org/u/plicht)\ **Replies:** 3\ **Last updated:** [February 8, 2022, 4:37pm UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878 "2022-02-08T16:37:25Z")
Dear biobakery-Team, I want to process paired-end reads with ShortBRED. To my knowledge, specifying 2 reads is not mentioned in the user manual. However, ShortBRED runs with 2 parsed reads and it was discussed in this t… --- ## [Precomputed SHORTBRED markers for dbCAN?](https://forum.biobakery.org/t/precomputed-shortbred-markers-for-dbcan/2981)
**Author:** [@isabel](https://forum.biobakery.org/u/isabel)\ **Replies:** 0\ **Last updated:** [January 11, 2022, 2:39pm UTC](https://forum.biobakery.org/t/precomputed-shortbred-markers-for-dbcan/2981 "2022-01-11T14:39:12Z")
Hi, My aim is to identify CAZymes in a metatranscriptomics dataset, and I was hoping to use SHORTBRED to do so. I was wondering if any precomputed markers are available for the CAZy database/dbCAN? I noticed some previo… --- ## [ShortBRED identify gives no markers](https://forum.biobakery.org/t/shortbred-identify-gives-no-markers/2353)
**Author:** [@plicht](https://forum.biobakery.org/u/plicht)\ **Replies:** 3\ **Last updated:** [January 4, 2022, 2:06pm UTC](https://forum.biobakery.org/t/shortbred-identify-gives-no-markers/2353 "2022-01-04T14:06:12Z")
Hello, I am trying to screen my metagenomic libraries for antimicrobial peptides present. Therfore I downloaded the database from APD3 (https://academic.oup.com/nar/article/44/D1/D1087/2503090) (https://wangapd3.com/APD… --- ## [Shortbred returns all zero count](https://forum.biobakery.org/t/shortbred-returns-all-zero-count/2698)
**Author:** [@zc1286](https://forum.biobakery.org/u/zc1286)\ **Replies:** 1\ **Last updated:** [November 5, 2021, 3:19pm UTC](https://forum.biobakery.org/t/shortbred-returns-all-zero-count/2698 "2021-11-05T15:19:46Z")
Dear shortbred developers, Good morning! Thank you for the fantastic bioinformatics tool! Recently I met a issue, which bother me for a long time, I hope I can get some issue or idea from you. I need to map metatransc… --- ## [Specifying strands in USEARCH within shortbred\_quantify](https://forum.biobakery.org/t/specifying-strands-in-usearch-within-shortbred-quantify/2659)
**Author:** [@LRB](https://forum.biobakery.org/u/LRB)\ **Replies:** 4\ **Last updated:** [October 24, 2021, 1:43am UTC](https://forum.biobakery.org/t/specifying-strands-in-usearch-within-shortbred-quantify/2659 "2021-10-24T01:43:01Z")
Hi ShortBRED team & users, I am trying to run shortbred\_quantify on some paired-end reads. I am using the following command : shortbred\_quantify.py --markers mymarkers.faa --wgs R1\_001-paired.fastq R2\_001-paired.fastq … --- ## [ShortBRED installation/dependency errors](https://forum.biobakery.org/t/shortbred-installation-dependency-errors/486)
**Author:** [@huananfshi](https://forum.biobakery.org/u/huananfshi)\ **Replies:** 3\ **Last updated:** [March 22, 2021, 12:54am UTC](https://forum.biobakery.org/t/shortbred-installation-dependency-errors/486 "2021-03-22T00:54:29Z")
When I tried to run shortbred\_identify.py, I got following dependency errors: shortbred\_identify.py --goi input\_prots.faa --ref ref\_prots.faa --markers mytestmarkers.faa --tmp example\_identify --usearch /usr/local/bin/… --- ## [How to add description information?](https://forum.biobakery.org/t/how-to-add-description-information/1083)
**Author:** [@wfgui](https://forum.biobakery.org/u/wfgui)\ **Replies:** 4\ **Last updated:** [September 16, 2021, 3:58pm UTC](https://forum.biobakery.org/t/how-to-add-description-information/1083 "2021-09-16T15:58:09Z")
Hi, I have downloaded Antibiotic Resistance Database (ARDB) Markers,and run shortbred\_quantify.py.This is the output reults: Family Count Hits TotMarkerLength 1112175A 0.0 0 68 AAA21889 0.0 0 95 AAA22905 0.0 0 44 AAA25… --- ## [UniRef90 or UniRef100 for building markers with ShortBRED-Identify?](https://forum.biobakery.org/t/uniref90-or-uniref100-for-building-markers-with-shortbred-identify/2263)
**Author:** [@ngocminhpham2601](https://forum.biobakery.org/u/ngocminhpham2601)\ **Replies:** 2\ **Last updated:** [July 9, 2021, 7:13pm UTC](https://forum.biobakery.org/t/uniref90-or-uniref100-for-building-markers-with-shortbred-identify/2263 "2021-07-09T19:13:53Z")
Hello, I am trying to build markers for antibiotic resistant genes using the updated CARD database. I see that there are different UniRef databases (50, 90, or 100). So, I wonder what would be the consequence of using o… --- ## [Fastq.gz file as input for ShortBRED?](https://forum.biobakery.org/t/fastq-gz-file-as-input-for-shortbred/2152)
**Author:** [@Thalla](https://forum.biobakery.org/u/Thalla)\ **Replies:** 2\ **Last updated:** [June 4, 2021, 9:37am UTC](https://forum.biobakery.org/t/fastq-gz-file-as-input-for-shortbred/2152 "2021-06-04T09:37:58Z")
Hi, I didn’t find any information about this and I’m worried that my results are not correct because I used ShortBRED with zipped files. So my question is, can I use fastq.gz files as input for ShortBRED quantify? Than… --- ## [Fatal Error: not enough memory, please set -M option greater than 1240](https://forum.biobakery.org/t/fatal-error-not-enough-memory-please-set-m-option-greater-than-1240/1985)
**Author:** [@aimirza](https://forum.biobakery.org/u/aimirza)\ **Replies:** 1\ **Last updated:** [April 29, 2021, 8:11pm UTC](https://forum.biobakery.org/t/fatal-error-not-enough-memory-please-set-m-option-greater-than-1240/1985 "2021-04-29T20:11:09Z")
Hi, I received the cd-hit error below while running shortbred\_identify.py. My command is shortbred\_identify.py --goi CAZyDB.07312020.fa --ref uniref90.fasta --markers CAZyDB\_uniref90.faa --tmp CAZyDB\_ShortBRED --threa… --- ## [Non-printing character 0x00 in sequence FASTA file ERROR](https://forum.biobakery.org/t/non-printing-character-0x00-in-sequence-fasta-file-error/1956)
**Author:** [@ekroeber](https://forum.biobakery.org/u/ekroeber)\ **Replies:** 9\ **Last updated:** [April 27, 2021, 12:24pm UTC](https://forum.biobakery.org/t/non-printing-character-0x00-in-sequence-fasta-file-error/1956 "2021-04-27T12:24:15Z")
Hi, I ran ShortBRED with contig files and the results were not as expected, so I wanted to run it again with the error corrected joined sequence fasta files, however, I always get a Non-printing character 0x00 in seque… --- ## [Blast db build fail](https://forum.biobakery.org/t/blast-db-build-fail/1827)
**Author:** [@aimirza](https://forum.biobakery.org/u/aimirza)\ **Replies:** 1\ **Last updated:** [March 25, 2021, 6:56pm UTC](https://forum.biobakery.org/t/blast-db-build-fail/1827 "2021-03-25T18:56:09Z")
Blast DB failed due to insufficient memory allocation. example\_identify/goidb.log says: Building a new DB, current time: 03/21/2021 20:37:02 New DB name: /home/amirza/CAZymes/example\_identify/clustdb/goidb New DB tit… --- ## [Reverse "normalize by number of reads in the sample"](https://forum.biobakery.org/t/reverse-normalize-by-number-of-reads-in-the-sample/1809)
**Author:** [@aimirza](https://forum.biobakery.org/u/aimirza)\ **Replies:** 0\ **Last updated:** [March 19, 2021, 1:49am UTC](https://forum.biobakery.org/t/reverse-normalize-by-number-of-reads-in-the-sample/1809 "2021-03-19T01:49:00Z")
Hi! How can we get counts not normalized by the number of reads in the sample, while still normalized by read length and sequence depth? Do I simply multiply the normalized counts by the total number of sequences in my m… --- ## [CARD pre-built marker](https://forum.biobakery.org/t/card-pre-built-marker/1784)
**Author:** [@Pascale](https://forum.biobakery.org/u/Pascale)\ **Replies:** 1\ **Last updated:** [March 15, 2021, 3:44pm UTC](https://forum.biobakery.org/t/card-pre-built-marker/1784 "2021-03-15T15:44:41Z")
The link on the official shortbred webpage https://huttenhower.sph.harvard.edu/shortbred/ to the pre-built CARD markers seems broken. https://bitbucket.org/biobakery/shortbred/downloads/ShortBRED\_CARD\_2017\_markers.faa… --- ## [Biopython, pip and Python-2 deprecation](https://forum.biobakery.org/t/biopython-pip-and-python-2-deprecation/1696)
**Author:** [@astrophys](https://forum.biobakery.org/u/astrophys)\ **Replies:** 1\ **Last updated:** [February 22, 2021, 12:13pm UTC](https://forum.biobakery.org/t/biopython-pip-and-python-2-deprecation/1696 "2021-02-22T12:13:21Z")
Initially I opened this issue on github, before I realized that this forum existed. Pip no longer supports Python-2 because Python-2 was deprecated 01/01/2020. Biopython is only available for Python-3 (at least via pip … --- ## [Normalize ShortBRED Reads](https://forum.biobakery.org/t/normalize-shortbred-reads/197)
**Author:** [@Joan\_Slonczewski](https://forum.biobakery.org/u/Joan_Slonczewski)\ **Replies:** 6\ **Last updated:** [February 5, 2021, 7:15pm UTC](https://forum.biobakery.org/t/normalize-shortbred-reads/197 "2021-02-05T19:15:31Z")
How do we normalize hit numbers to the sample? Is it reasonable to normalize hits to the number of reads in the FASTA file? --- ## [Fatal error Usearch 64-bit needed](https://forum.biobakery.org/t/fatal-error-usearch-64-bit-needed/1634)
**Author:** [@edisagar](https://forum.biobakery.org/u/edisagar)\ **Replies:** 0\ **Last updated:** [January 31, 2021, 3:52pm UTC](https://forum.biobakery.org/t/fatal-error-usearch-64-bit-needed/1634 "2021-01-31T15:52:30Z")
Hello, I am using shortBred\_quantify --genome, I have a fatal error: Memory limit of 32-bit process exceeded, 64-bit build required ('Using this version of usearch: ‘, u’v11.0.667’) It is a pity because it is impossi… --- ## [ImportError: Bio.Alphabet has been removed from Biopython](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133)
**Author:** [@paulokoroc](https://forum.biobakery.org/u/paulokoroc)\ **Replies:** 2\ **Last updated:** [November 27, 2020, 4:51am UTC](https://forum.biobakery.org/t/importerror-bio-alphabet-has-been-removed-from-biopython/1133 "2020-11-27T04:51:58Z")
Hi, I tried running this shortbred command; shortbred\_identify.py --goi tonB.faa --ref tutorial\_ref\_prots.faa --markers mymarkers.faa --tmp example\_identify and I got this error: Traceback (most recent call last): F… --- ## [Usearch\_local for quantification](https://forum.biobakery.org/t/usearch-local-for-quantification/901)
**Author:** [@Yishay](https://forum.biobakery.org/u/Yishay)\ **Replies:** 1\ **Last updated:** [August 28, 2020, 6:01pm UTC](https://forum.biobakery.org/t/usearch-local-for-quantification/901 "2020-08-28T18:01:45Z")
Hi, I’m using shortBred\_quantify in order to quantify microbial genes in several metagenomic samples. Since I’m having some difficulties (mainly runtime and costs) I’m wondering what were the considerations of choosing… --- ## [Shortbred identify performance with CARD and Uniref90](https://forum.biobakery.org/t/shortbred-identify-performance-with-card-and-uniref90/797)
**Author:** [@Erwan](https://forum.biobakery.org/u/Erwan)\ **Replies:** 0\ **Last updated:** [July 30, 2020, 10:00am UTC](https://forum.biobakery.org/t/shortbred-identify-performance-with-card-and-uniref90/797 "2020-07-30T10:00:14Z")
Hi, I want to create a set of markers with shortbred-identify using the newly released CARD database (May 2020 version) as my proteins of interest and Uniref90 as my reference proteins sequences. It seems that the proc… --- ## [ARO id to antibiotics clusters](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628)
**Author:** [@Qiuyu\_Jing](https://forum.biobakery.org/u/Qiuyu_Jing)\ **Replies:** 2\ **Last updated:** [June 25, 2020, 5:28pm UTC](https://forum.biobakery.org/t/aro-id-to-antibiotics-clusters/628 "2020-06-25T17:28:14Z")
Hi, May i know that how i can cluster the antibiotics families quantified from ShortBRED to larger antibiotics resistant group based on ARO id? like the heatmap in 2015-paper? --- ## [Creating markers after blasting](https://forum.biobakery.org/t/creating-markers-after-blasting/263)
**Author:** [@luayou](https://forum.biobakery.org/u/luayou)\ **Replies:** 5\ **Last updated:** [April 1, 2020, 3:24pm UTC](https://forum.biobakery.org/t/creating-markers-after-blasting/263 "2020-04-01T15:24:23Z")
Hi there! I am trying to create some markers, and I am having this problem https://groups.google.com/forum/#!topic/shortbred-users/paafRPifkM8 I have already run blast of my proteins against all uniref90 (blast/2.2.29)… [Previous page](https://forum.biobakery.org/c/microbial-community-profiling/shortbred/24.md)