unable to gmap the transcripts and output alignments:
Entering edit mode
6 days ago

HI I have extracted the *.fa files into their respective directories by using below command: gmap_build -D can1 -d can1 HI.4746.005.Index_13.Black_Jack_Spice_scaffold.fa

Jun 22 23:41 all_tps.fasta Jun 22 23:41 can1 Jun 22 23:42 can2 Jun 22 23:43 can3 Jun 22 23:37 HI.4746.005.Index_13.Black_Jack_Spice_scaffold.fa Jun 22 23:37 HI.4746.005.Index_15.CBD_God_Bud_Spice_scaffold.fa Jun 22 23:37 HI.4746.005.Index_16.Cristal_Limit_MSC_28_scaffold.fa

Now according to below document https://github.com/slavailn/terpene_synthase_project/commit/ae9504135d44395175b8e6bc7a63f37763f8d94a Now I need to map the transcripts and output alignments: gmap -t 4 -A -D <index_directory> -d <genome_name> <cds.fasta> > <gmap_out.txt>

what values I should put against index_director, genome_name and cds.fasta. I try below command but it stucks at "Reading from stdin"

gmap -A -D can1/can1 -d all_tps.fasta Note: gmap.avx2 does not exist. For faster speed, may want to compile package on an AVX2 machine GMAP version 2021-08-25 called with args: gmap.sse42 -A -D can1/can1 -d all_tps.fasta Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1 Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17 Finished checking compiler assumptions Reading from stdin

gmap • 87 views
Entering edit mode
6 days ago
colindaven ★ 3.9k

You need to pass the fasta file in properly, it is waiting for the input

I used a command like this (was a couple of years ago now)

gmap -f gff3_gene -D /lager2/rcug/seqres/HS/gmap/hg19_gmap -d hg19_gmap -B 5 -t 16 --intronlength=150000 --totallength=1000000 --npaths 1 -p 3 in.fa > in.fa.gff3

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